organic compounds
Apilimod
aDivision of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, USA, and bUCSD Crystallography Facility, University of California, San Diego, La Jolla, California 92093, USA
*Correspondence e-mail: patrick.morris@mail.nih.gov
Apilimod {systematic name: N-[(E)-(3-methylbenzylidene)amino]-6-(morpholin-4-yl)-2-[2-(pyridin-2-yl)ethoxy]pyrimidin-4-amine}, C23H26N6O2, a molecule of interest for its antiviral properties, was acquired from several different commercial vendors. Analysis of several commercial batches had led to some ambiguity over the exact structure. In order to remove any ambiguity, the structure was confirmed by X-ray crystallography. In addition, the NMR spectra are provided as reference material for future investigations.
Keywords: crystal structure; hydrogen bonding; structural confirmation; NMR; antiviral.
CCDC reference: 1526003
Structure description
Apilimod is an inhibitor of IL12/23 production, originally developed for the treatment of rheumatoid arthritis by Synta pharmaceuticals (Ono et al., 2003). More recently, it was disclosed that apilimod acts as an inhibitor of PIKFyve, a key enzyme which phosphorylates phosphatidylinositol 3-phosphate to phosphatidylinositol 3,5-diphosphate (Cai et al., 2013). Currently, apilimod is under investigation for its antiviral activity, and recent work has shown that it has pronounced activity against the ebola virus (Cunningham, 2016; Lichenstein et al. 2016). However, significantly different antiviral activity was noted between different commercial batches of apilimod, which led us to a more thorough chemical characterization of the pharmaceutical. Upon further examination, it was found that there were several commercial batches where the ethoxypyridyl substituent and the morpholine substituent on the core pyrimidine ring were switched, which led to sharply diminished antiviral activity. In order to confirm the correct structure, and ensure the most active batch of apilimod was actually apilimod, single-crystal X-ray crystallography on the most biologically active commercial batch of apilimod was utilized in order to obtain an unambiguous structure.
Structural analysis shows the presence of two crystallographically independent molecules, whose connectivity matches that of the published structure (Fig. 1). Notably, the presence of intermolecular hydrogen bonding between the NH of the hydrazine functionality and the pyrimidine nitrogen atom is present, with a hydrogen-bond length of 3.0626 (16) Å apparent (Table 1). The structures of the two molecules differ slightly in several ways, with the most distinct point of deviation being the O1—C17—C18 angle, which measures 106.76 (10)°, while the corresponding O1′—C17′—C18′ angle is 111.53 (11)°. As expected, in both structures the imine bond maintains an (E) geometry.
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Synthesis and crystallization
Apilimod was provided by Axon Medchem (Reston, VA) and synthesized via the route outlined in the original patent (Ono et al., 2003). The compound was crystallized as colorless blocks by dissolving a sample of approximately 1 mg in 0.35 ml dichloromethane and vapor diffusing the sample with pentane over two days. In addition to X-ray crystallography, the compound was characterized by 1H NMR and 13C NMR. For reference, those values and spectra are reproduced here (Figs. 2 and 3). Notably, apilimod shows the morpholine peaks as two distinct peaks at 3.78 and 3.64 p.p.m. This is a key difference, as the incorrect regioisomeric structure shows a single morpholine peak.
1H NMR (400 MHz, CDCl3) δ 8.65 (s, 1H), 8.54 (ddd, J = 4.9, 1.9, 0.9 Hz, 1H), 7.74 (s, 1H), 7.60 (td, J = 7.7, 1.9 Hz, 1H), 7.54–7.39 (m, 2H), 7.32–7.23 (m, 1H), 7.20–7.08 (m, 2H), 6.08 (s, 1H), 4.65 (t, J = 6.9 Hz, 2H), 3.78 (dd, J = 5.7, 4.0 Hz, 4H), 3.64 (dd, J = 5.7, 4.1 Hz, 4H), 3.26 (t, J = 6.9 Hz, 2H), 2.38 (s, 3H).
13C NMR (101 MHz, CDCl3) δ 164.7, 163.9, 162.7, 158.7, 149.4, 142.0, 138.5, 136.7, 134.3, 130.5, 128.7, 127.4, 124.2, 124.0, 121.7, 76.5, 66.8, 66.2, 44.8, 37.9, 21.5.
Refinement
Crystal data, data collection and structural .
details are summarized in Table 2Structural data
CCDC reference: 1526003
https://doi.org/10.1107/S2414314617006939/zl4016sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314617006939/zl4016Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2414314617006939/zl4016Isup3.cml
Data collection: APEX2 (Bruker, 2014); cell
SAINT (Bruker, 2013); data reduction: SAINT (Bruker, 2013); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL (Sheldrick, 2015b); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).C23H26N6O2 | F(000) = 1776 |
Mr = 418.50 | Dx = 1.287 Mg m−3 |
Monoclinic, P21/c | Cu Kα radiation, λ = 1.54178 Å |
a = 14.9353 (5) Å | Cell parameters from 9651 reflections |
b = 15.0367 (5) Å | θ = 4.2–68.5° |
c = 19.4231 (7) Å | µ = 0.69 mm−1 |
β = 98.130 (2)° | T = 100 K |
V = 4318.2 (3) Å3 | Block, colourless |
Z = 8 | 0.25 × 0.21 × 0.19 mm |
Bruker X8 APEXII diffractometer | 7881 independent reflections |
Radiation source: Micro Focus Rotating Anode, Bruker Microstar FR-592 | 6816 reflections with I > 2σ(I) |
Double Bounce Multilayer Mirrors monochromator | Rint = 0.038 |
Detector resolution: 7.9 pixels mm-1 | θmax = 68.5°, θmin = 3.0° |
ω and φ scans | h = −17→18 |
Absorption correction: multi-scan (SADABS; Bruker, 2014) | k = −18→17 |
Tmin = 0.228, Tmax = 0.320 | l = −23→22 |
50098 measured reflections |
Refinement on F2 | Primary atom site location: dual |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.038 | Hydrogen site location: mixed |
wR(F2) = 0.103 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.04 | w = 1/[σ2(Fo2) + (0.0527P)2 + 1.2958P] where P = (Fo2 + 2Fc2)/3 |
7881 reflections | (Δ/σ)max = 0.001 |
569 parameters | Δρmax = 0.29 e Å−3 |
2 restraints | Δρmin = −0.22 e Å−3 |
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. |
Refinement. All nonhydrogen atoms were refined anisotropically by full-matrix least-squares (SHELXL2014). All carbon bonded hydrogen atoms were placed using a riding model. Their positions were constrained relative to their parent atom using the appropriate HFIX command in SHELXL2014. All other hydrogen atoms (H-bonding) were located in difference mapa. Their relative positions were restrained using DFIX commands and their thermal parameters freely refined. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.34895 (6) | 0.49264 (6) | 0.73640 (4) | 0.0263 (2) | |
O2 | 0.79885 (6) | 0.64234 (7) | 0.75289 (5) | 0.0313 (2) | |
N1 | 0.35964 (8) | 0.58848 (8) | 0.51765 (6) | 0.0277 (2) | |
H1 | 0.2990 (9) | 0.5779 (11) | 0.5100 (8) | 0.031 (4)* | |
N2 | 0.35530 (7) | 0.54354 (7) | 0.62910 (5) | 0.0247 (2) | |
N3 | 0.48892 (7) | 0.53447 (7) | 0.71298 (5) | 0.0240 (2) | |
N4 | 0.62723 (8) | 0.58340 (8) | 0.68986 (6) | 0.0301 (3) | |
N5 | 0.40438 (7) | 0.62175 (7) | 0.46652 (5) | 0.0255 (2) | |
N6 | 0.41499 (8) | 0.34602 (8) | 0.92805 (6) | 0.0325 (3) | |
C1 | 0.40704 (9) | 0.57268 (9) | 0.58201 (6) | 0.0242 (3) | |
C2 | 0.49980 (9) | 0.58574 (9) | 0.59747 (7) | 0.0263 (3) | |
H2 | 0.5349 | 0.6060 | 0.5634 | 0.032* | |
C3 | 0.53853 (9) | 0.56760 (9) | 0.66551 (7) | 0.0245 (3) | |
C4 | 0.40211 (9) | 0.52482 (8) | 0.69093 (6) | 0.0232 (3) | |
C5 | 0.35753 (9) | 0.63339 (9) | 0.40663 (7) | 0.0256 (3) | |
H5 | 0.2947 | 0.6200 | 0.4001 | 0.031* | |
C6 | 0.39974 (9) | 0.66702 (9) | 0.34817 (6) | 0.0241 (3) | |
C7 | 0.34625 (9) | 0.67965 (9) | 0.28399 (7) | 0.0250 (3) | |
H7 | 0.2829 | 0.6698 | 0.2802 | 0.030* | |
C8 | 0.38319 (9) | 0.70632 (9) | 0.22533 (7) | 0.0262 (3) | |
C9 | 0.47498 (9) | 0.72490 (9) | 0.23255 (7) | 0.0286 (3) | |
H9 | 0.5014 | 0.7447 | 0.1935 | 0.034* | |
C10 | 0.52836 (9) | 0.71475 (10) | 0.29639 (7) | 0.0297 (3) | |
H10 | 0.5909 | 0.7290 | 0.3008 | 0.036* | |
C11 | 0.49266 (9) | 0.68427 (9) | 0.35387 (7) | 0.0262 (3) | |
H11 | 0.5307 | 0.6751 | 0.3968 | 0.031* | |
C12 | 0.32505 (10) | 0.71098 (10) | 0.15531 (7) | 0.0342 (3) | |
H12A | 0.3463 | 0.6672 | 0.1239 | 0.051* | |
H12B | 0.3289 | 0.7707 | 0.1358 | 0.051* | |
H12C | 0.2621 | 0.6981 | 0.1607 | 0.051* | |
C13 | 0.68901 (9) | 0.62522 (10) | 0.64810 (7) | 0.0313 (3) | |
H13A | 0.6545 | 0.6593 | 0.6096 | 0.038* | |
H13B | 0.7249 | 0.5792 | 0.6278 | 0.038* | |
C14 | 0.75126 (10) | 0.68681 (10) | 0.69423 (7) | 0.0327 (3) | |
H14A | 0.7954 | 0.7134 | 0.6667 | 0.039* | |
H14B | 0.7152 | 0.7358 | 0.7105 | 0.039* | |
C15 | 0.67356 (9) | 0.53962 (9) | 0.75186 (7) | 0.0286 (3) | |
H15A | 0.7084 | 0.4882 | 0.7381 | 0.034* | |
H15B | 0.6285 | 0.5172 | 0.7804 | 0.034* | |
C16 | 0.73665 (9) | 0.60377 (10) | 0.79406 (7) | 0.0301 (3) | |
H16A | 0.7009 | 0.6515 | 0.8124 | 0.036* | |
H16B | 0.7707 | 0.5721 | 0.8342 | 0.036* | |
C17 | 0.39265 (9) | 0.47784 (9) | 0.80631 (6) | 0.0267 (3) | |
H17A | 0.4170 | 0.5344 | 0.8274 | 0.032* | |
H17B | 0.4432 | 0.4352 | 0.8065 | 0.032* | |
C18 | 0.32146 (9) | 0.44048 (9) | 0.84671 (7) | 0.0276 (3) | |
H18A | 0.2722 | 0.4844 | 0.8474 | 0.033* | |
H18B | 0.2952 | 0.3857 | 0.8238 | 0.033* | |
C19 | 0.36342 (9) | 0.41962 (9) | 0.91997 (7) | 0.0275 (3) | |
C20 | 0.35200 (12) | 0.47483 (10) | 0.97472 (8) | 0.0402 (4) | |
H20 | 0.3147 | 0.5261 | 0.9673 | 0.048* | |
C21 | 0.39550 (14) | 0.45474 (12) | 1.04074 (8) | 0.0497 (4) | |
H21 | 0.3889 | 0.4922 | 1.0791 | 0.060* | |
C22 | 0.44831 (12) | 0.37974 (11) | 1.04972 (8) | 0.0435 (4) | |
H22 | 0.4786 | 0.3641 | 1.0944 | 0.052* | |
C23 | 0.45640 (10) | 0.32763 (11) | 0.99250 (8) | 0.0378 (3) | |
H23 | 0.4932 | 0.2759 | 0.9990 | 0.045* | |
O1' | 0.14106 (6) | 0.53264 (6) | 0.39198 (4) | 0.0257 (2) | |
O2' | −0.28751 (7) | 0.71945 (7) | 0.41569 (5) | 0.0376 (2) | |
N1' | 0.16456 (8) | 0.61288 (8) | 0.61828 (5) | 0.0257 (2) | |
H1' | 0.2222 (10) | 0.5909 (12) | 0.6227 (9) | 0.039 (5)* | |
N2' | 0.15315 (7) | 0.57612 (7) | 0.50314 (5) | 0.0231 (2) | |
N3' | 0.01224 (7) | 0.58701 (7) | 0.42790 (5) | 0.0227 (2) | |
N4' | −0.11443 (7) | 0.64966 (8) | 0.46210 (6) | 0.0266 (2) | |
N5' | 0.12430 (8) | 0.63141 (7) | 0.67570 (5) | 0.0257 (2) | |
N6' | 0.09634 (8) | 0.58164 (9) | 0.16839 (6) | 0.0349 (3) | |
C1' | 0.11114 (9) | 0.60824 (8) | 0.55523 (6) | 0.0229 (3) | |
C2' | 0.02131 (9) | 0.63494 (9) | 0.54633 (7) | 0.0240 (3) | |
H2' | −0.0058 | 0.6597 | 0.5834 | 0.029* | |
C3' | −0.02685 (9) | 0.62349 (8) | 0.48016 (6) | 0.0226 (3) | |
C4' | 0.09872 (9) | 0.56733 (8) | 0.44311 (6) | 0.0223 (3) | |
C5' | 0.17579 (9) | 0.63390 (9) | 0.73411 (7) | 0.0270 (3) | |
H5' | 0.2391 | 0.6254 | 0.7358 | 0.032* | |
C6' | 0.13749 (10) | 0.64987 (9) | 0.79854 (7) | 0.0277 (3) | |
C7' | 0.19622 (10) | 0.66530 (9) | 0.85979 (7) | 0.0300 (3) | |
H7' | 0.2597 | 0.6643 | 0.8590 | 0.036* | |
C8' | 0.16319 (11) | 0.68225 (9) | 0.92267 (7) | 0.0326 (3) | |
C9' | 0.07049 (11) | 0.68297 (10) | 0.92257 (7) | 0.0347 (3) | |
H9' | 0.0470 | 0.6949 | 0.9646 | 0.042* | |
C10' | 0.01152 (11) | 0.66672 (10) | 0.86247 (8) | 0.0345 (3) | |
H10' | −0.0518 | 0.6670 | 0.8637 | 0.041* | |
C11' | 0.04427 (10) | 0.65000 (9) | 0.80046 (7) | 0.0304 (3) | |
H11' | 0.0034 | 0.6387 | 0.7593 | 0.037* | |
C12' | 0.22766 (12) | 0.69882 (11) | 0.98798 (8) | 0.0401 (4) | |
H12D | 0.2258 | 0.6485 | 1.0198 | 0.060* | |
H12E | 0.2102 | 0.7534 | 1.0103 | 0.060* | |
H12F | 0.2891 | 0.7054 | 0.9765 | 0.060* | |
C13' | −0.16680 (10) | 0.69041 (11) | 0.51118 (7) | 0.0329 (3) | |
H13C | −0.1259 | 0.7202 | 0.5487 | 0.040* | |
H13D | −0.2015 | 0.6443 | 0.5324 | 0.040* | |
C14' | −0.23092 (10) | 0.75771 (11) | 0.47298 (8) | 0.0366 (3) | |
H14C | −0.2691 | 0.7834 | 0.5057 | 0.044* | |
H14D | −0.1954 | 0.8066 | 0.4561 | 0.044* | |
C15' | −0.17133 (9) | 0.61136 (9) | 0.40220 (7) | 0.0283 (3) | |
H15C | −0.2069 | 0.5613 | 0.4174 | 0.034* | |
H15D | −0.1330 | 0.5881 | 0.3687 | 0.034* | |
C16' | −0.23406 (10) | 0.68121 (10) | 0.36784 (7) | 0.0337 (3) | |
H16C | −0.1983 | 0.7285 | 0.3490 | 0.040* | |
H16D | −0.2744 | 0.6544 | 0.3285 | 0.040* | |
C17' | 0.08812 (9) | 0.52409 (9) | 0.32382 (6) | 0.0252 (3) | |
H17C | 0.0283 | 0.4984 | 0.3287 | 0.030* | |
H17D | 0.1191 | 0.4829 | 0.2952 | 0.030* | |
C18' | 0.07489 (10) | 0.61360 (9) | 0.28716 (7) | 0.0291 (3) | |
H18C | 0.0332 | 0.6506 | 0.3103 | 0.035* | |
H18D | 0.1337 | 0.6449 | 0.2907 | 0.035* | |
C19' | 0.03685 (9) | 0.60182 (9) | 0.21177 (7) | 0.0275 (3) | |
C20' | −0.05490 (10) | 0.60954 (11) | 0.18879 (8) | 0.0372 (3) | |
H20' | −0.0956 | 0.6231 | 0.2207 | 0.045* | |
C21' | −0.08694 (11) | 0.59735 (12) | 0.11920 (8) | 0.0428 (4) | |
H21' | −0.1497 | 0.6025 | 0.1026 | 0.051* | |
C22' | −0.02636 (12) | 0.57763 (12) | 0.07445 (8) | 0.0411 (4) | |
H22' | −0.0460 | 0.5694 | 0.0262 | 0.049* | |
C23' | 0.06354 (11) | 0.57011 (12) | 0.10134 (8) | 0.0413 (4) | |
H23' | 0.1051 | 0.5558 | 0.0702 | 0.050* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0243 (5) | 0.0343 (5) | 0.0202 (4) | −0.0029 (4) | 0.0029 (3) | 0.0037 (4) |
O2 | 0.0267 (5) | 0.0350 (5) | 0.0321 (5) | −0.0038 (4) | 0.0037 (4) | −0.0031 (4) |
N1 | 0.0222 (6) | 0.0399 (7) | 0.0209 (5) | −0.0032 (5) | 0.0028 (4) | 0.0033 (5) |
N2 | 0.0239 (5) | 0.0290 (6) | 0.0211 (5) | −0.0002 (4) | 0.0032 (4) | 0.0015 (4) |
N3 | 0.0234 (5) | 0.0251 (6) | 0.0232 (5) | −0.0010 (4) | 0.0020 (4) | 0.0013 (4) |
N4 | 0.0224 (6) | 0.0394 (7) | 0.0279 (6) | −0.0029 (5) | 0.0013 (5) | 0.0089 (5) |
N5 | 0.0267 (6) | 0.0297 (6) | 0.0207 (5) | −0.0007 (5) | 0.0055 (4) | 0.0010 (4) |
N6 | 0.0327 (6) | 0.0346 (7) | 0.0309 (6) | 0.0007 (5) | 0.0071 (5) | 0.0060 (5) |
C1 | 0.0262 (7) | 0.0251 (6) | 0.0214 (6) | 0.0011 (5) | 0.0035 (5) | −0.0006 (5) |
C2 | 0.0247 (7) | 0.0311 (7) | 0.0237 (6) | −0.0001 (5) | 0.0056 (5) | 0.0024 (5) |
C3 | 0.0245 (6) | 0.0238 (6) | 0.0252 (6) | 0.0007 (5) | 0.0034 (5) | 0.0008 (5) |
C4 | 0.0249 (6) | 0.0231 (6) | 0.0220 (6) | −0.0014 (5) | 0.0044 (5) | −0.0008 (5) |
C5 | 0.0240 (6) | 0.0293 (7) | 0.0236 (6) | −0.0013 (5) | 0.0038 (5) | −0.0009 (5) |
C6 | 0.0264 (7) | 0.0239 (6) | 0.0221 (6) | −0.0008 (5) | 0.0038 (5) | −0.0019 (5) |
C7 | 0.0239 (6) | 0.0249 (7) | 0.0259 (6) | −0.0006 (5) | 0.0024 (5) | 0.0001 (5) |
C8 | 0.0321 (7) | 0.0226 (6) | 0.0234 (6) | 0.0023 (5) | 0.0023 (5) | 0.0006 (5) |
C9 | 0.0331 (7) | 0.0285 (7) | 0.0256 (7) | −0.0010 (6) | 0.0086 (5) | 0.0030 (5) |
C10 | 0.0242 (7) | 0.0339 (7) | 0.0314 (7) | −0.0026 (5) | 0.0055 (5) | 0.0004 (6) |
C11 | 0.0258 (7) | 0.0289 (7) | 0.0235 (6) | −0.0007 (5) | 0.0018 (5) | −0.0013 (5) |
C12 | 0.0379 (8) | 0.0400 (8) | 0.0235 (7) | 0.0014 (6) | 0.0000 (6) | 0.0045 (6) |
C13 | 0.0246 (7) | 0.0401 (8) | 0.0294 (7) | −0.0021 (6) | 0.0046 (5) | 0.0053 (6) |
C14 | 0.0313 (7) | 0.0322 (8) | 0.0356 (8) | −0.0016 (6) | 0.0086 (6) | 0.0018 (6) |
C15 | 0.0262 (7) | 0.0297 (7) | 0.0286 (7) | 0.0003 (5) | −0.0006 (5) | 0.0041 (5) |
C16 | 0.0299 (7) | 0.0314 (7) | 0.0290 (7) | −0.0005 (6) | 0.0038 (6) | −0.0009 (6) |
C17 | 0.0278 (7) | 0.0321 (7) | 0.0198 (6) | −0.0021 (5) | 0.0015 (5) | 0.0031 (5) |
C18 | 0.0292 (7) | 0.0288 (7) | 0.0252 (7) | −0.0014 (5) | 0.0053 (5) | 0.0028 (5) |
C19 | 0.0301 (7) | 0.0270 (7) | 0.0261 (7) | −0.0042 (5) | 0.0068 (5) | 0.0046 (5) |
C20 | 0.0618 (10) | 0.0292 (8) | 0.0303 (8) | 0.0036 (7) | 0.0090 (7) | 0.0023 (6) |
C21 | 0.0840 (13) | 0.0380 (9) | 0.0266 (8) | −0.0095 (9) | 0.0064 (8) | −0.0022 (7) |
C22 | 0.0544 (10) | 0.0415 (9) | 0.0308 (8) | −0.0155 (8) | −0.0066 (7) | 0.0106 (7) |
C23 | 0.0334 (8) | 0.0400 (8) | 0.0392 (8) | −0.0015 (6) | 0.0019 (6) | 0.0129 (7) |
O1' | 0.0230 (4) | 0.0346 (5) | 0.0192 (4) | 0.0046 (4) | 0.0018 (3) | −0.0038 (4) |
O2' | 0.0268 (5) | 0.0451 (6) | 0.0387 (6) | 0.0091 (4) | −0.0036 (4) | −0.0094 (5) |
N1' | 0.0241 (6) | 0.0339 (6) | 0.0190 (5) | 0.0018 (5) | 0.0030 (4) | −0.0023 (4) |
N2' | 0.0233 (5) | 0.0268 (6) | 0.0192 (5) | 0.0002 (4) | 0.0025 (4) | −0.0007 (4) |
N3' | 0.0223 (5) | 0.0244 (5) | 0.0212 (5) | 0.0009 (4) | 0.0028 (4) | −0.0004 (4) |
N4' | 0.0226 (6) | 0.0355 (6) | 0.0217 (5) | 0.0044 (5) | 0.0026 (4) | −0.0027 (5) |
N5' | 0.0302 (6) | 0.0274 (6) | 0.0199 (5) | 0.0002 (5) | 0.0050 (4) | −0.0014 (4) |
N6' | 0.0321 (6) | 0.0459 (7) | 0.0277 (6) | 0.0008 (5) | 0.0071 (5) | 0.0016 (5) |
C1' | 0.0257 (6) | 0.0224 (6) | 0.0204 (6) | −0.0021 (5) | 0.0027 (5) | 0.0010 (5) |
C2' | 0.0258 (6) | 0.0254 (6) | 0.0214 (6) | 0.0015 (5) | 0.0052 (5) | −0.0001 (5) |
C3' | 0.0225 (6) | 0.0221 (6) | 0.0234 (6) | 0.0001 (5) | 0.0045 (5) | 0.0023 (5) |
C4' | 0.0233 (6) | 0.0228 (6) | 0.0209 (6) | −0.0002 (5) | 0.0039 (5) | 0.0002 (5) |
C5' | 0.0303 (7) | 0.0274 (7) | 0.0232 (6) | 0.0012 (5) | 0.0028 (5) | −0.0008 (5) |
C6' | 0.0388 (8) | 0.0223 (6) | 0.0213 (6) | 0.0010 (5) | 0.0021 (5) | −0.0005 (5) |
C7' | 0.0378 (8) | 0.0260 (7) | 0.0255 (7) | 0.0011 (6) | 0.0017 (6) | 0.0001 (5) |
C8' | 0.0527 (9) | 0.0219 (7) | 0.0218 (7) | 0.0025 (6) | −0.0002 (6) | −0.0001 (5) |
C9' | 0.0498 (9) | 0.0288 (7) | 0.0276 (7) | 0.0044 (6) | 0.0126 (6) | 0.0011 (6) |
C10' | 0.0399 (8) | 0.0319 (8) | 0.0333 (8) | 0.0011 (6) | 0.0108 (6) | 0.0001 (6) |
C11' | 0.0366 (8) | 0.0275 (7) | 0.0276 (7) | −0.0010 (6) | 0.0060 (6) | −0.0010 (5) |
C12' | 0.0543 (10) | 0.0376 (8) | 0.0264 (7) | 0.0030 (7) | −0.0016 (7) | −0.0041 (6) |
C13' | 0.0284 (7) | 0.0446 (8) | 0.0266 (7) | 0.0059 (6) | 0.0066 (6) | −0.0031 (6) |
C14' | 0.0304 (7) | 0.0437 (9) | 0.0340 (8) | 0.0086 (6) | −0.0008 (6) | −0.0090 (6) |
C15' | 0.0251 (7) | 0.0308 (7) | 0.0280 (7) | 0.0002 (5) | 0.0006 (5) | −0.0021 (5) |
C16' | 0.0336 (8) | 0.0361 (8) | 0.0295 (7) | 0.0056 (6) | −0.0024 (6) | −0.0037 (6) |
C17' | 0.0254 (6) | 0.0305 (7) | 0.0191 (6) | 0.0015 (5) | 0.0012 (5) | −0.0044 (5) |
C18' | 0.0315 (7) | 0.0309 (7) | 0.0248 (7) | −0.0020 (6) | 0.0034 (5) | −0.0014 (5) |
C19' | 0.0302 (7) | 0.0277 (7) | 0.0250 (7) | −0.0009 (5) | 0.0055 (5) | 0.0022 (5) |
C20' | 0.0297 (7) | 0.0537 (10) | 0.0290 (7) | 0.0014 (7) | 0.0069 (6) | 0.0074 (7) |
C21' | 0.0316 (8) | 0.0612 (11) | 0.0335 (8) | −0.0050 (7) | −0.0020 (6) | 0.0124 (7) |
C22' | 0.0485 (9) | 0.0504 (10) | 0.0227 (7) | −0.0061 (7) | −0.0009 (6) | 0.0052 (6) |
C23' | 0.0451 (9) | 0.0549 (10) | 0.0257 (7) | 0.0013 (7) | 0.0115 (6) | −0.0005 (7) |
O1—C4 | 1.3575 (15) | O1'—C4' | 1.3549 (15) |
O1—C17 | 1.4381 (15) | O1'—C17' | 1.4486 (15) |
O2—C14 | 1.4217 (17) | O2'—C14' | 1.4204 (17) |
O2—C16 | 1.4313 (17) | O2'—C16' | 1.4289 (17) |
N1—H1 | 0.911 (13) | N1'—H1' | 0.915 (14) |
N1—N5 | 1.3678 (15) | N1'—N5' | 1.3684 (15) |
N1—C1 | 1.3673 (17) | N1'—C1' | 1.3656 (16) |
N2—C1 | 1.3513 (17) | N2'—C1' | 1.3527 (16) |
N2—C4 | 1.3314 (17) | N2'—C4' | 1.3303 (16) |
N3—C3 | 1.3566 (17) | N3'—C3' | 1.3564 (16) |
N3—C4 | 1.3147 (17) | N3'—C4' | 1.3172 (17) |
N4—C3 | 1.3631 (18) | N4'—C3' | 1.3635 (17) |
N4—C13 | 1.4548 (17) | N4'—C13' | 1.4515 (17) |
N4—C15 | 1.4583 (17) | N4'—C15' | 1.4587 (17) |
N5—C5 | 1.2819 (17) | N5'—C5' | 1.2781 (17) |
N6—C19 | 1.3448 (19) | N6'—C19' | 1.3429 (18) |
N6—C23 | 1.3443 (19) | N6'—C23' | 1.3363 (19) |
C1—C2 | 1.3893 (19) | C1'—C2' | 1.3877 (18) |
C2—H2 | 0.9500 | C2'—H2' | 0.9500 |
C2—C3 | 1.3925 (18) | C2'—C3' | 1.3918 (18) |
C5—H5 | 0.9500 | C5'—H5' | 0.9500 |
C5—C6 | 1.4645 (18) | C5'—C6' | 1.4675 (18) |
C6—C7 | 1.3952 (18) | C6'—C7' | 1.3940 (19) |
C6—C11 | 1.4008 (19) | C6'—C11' | 1.398 (2) |
C7—H7 | 0.9500 | C7'—H7' | 0.9500 |
C7—C8 | 1.3932 (18) | C7'—C8' | 1.404 (2) |
C8—C9 | 1.387 (2) | C8'—C9' | 1.384 (2) |
C8—C12 | 1.5083 (18) | C8'—C12' | 1.501 (2) |
C9—H9 | 0.9500 | C9'—H9' | 0.9500 |
C9—C10 | 1.3843 (19) | C9'—C10' | 1.381 (2) |
C10—H10 | 0.9500 | C10'—H10' | 0.9500 |
C10—C11 | 1.3818 (19) | C10'—C11' | 1.386 (2) |
C11—H11 | 0.9500 | C11'—H11' | 0.9500 |
C12—H12A | 0.9800 | C12'—H12D | 0.9800 |
C12—H12B | 0.9800 | C12'—H12E | 0.9800 |
C12—H12C | 0.9800 | C12'—H12F | 0.9800 |
C13—H13A | 0.9900 | C13'—H13C | 0.9900 |
C13—H13B | 0.9900 | C13'—H13D | 0.9900 |
C13—C14 | 1.513 (2) | C13'—C14' | 1.513 (2) |
C14—H14A | 0.9900 | C14'—H14C | 0.9900 |
C14—H14B | 0.9900 | C14'—H14D | 0.9900 |
C15—H15A | 0.9900 | C15'—H15C | 0.9900 |
C15—H15B | 0.9900 | C15'—H15D | 0.9900 |
C15—C16 | 1.5071 (19) | C15'—C16' | 1.500 (2) |
C16—H16A | 0.9900 | C16'—H16C | 0.9900 |
C16—H16B | 0.9900 | C16'—H16D | 0.9900 |
C17—H17A | 0.9900 | C17'—H17C | 0.9900 |
C17—H17B | 0.9900 | C17'—H17D | 0.9900 |
C17—C18 | 1.5159 (18) | C17'—C18' | 1.5225 (19) |
C18—H18A | 0.9900 | C18'—H18C | 0.9900 |
C18—H18B | 0.9900 | C18'—H18D | 0.9900 |
C18—C19 | 1.5045 (18) | C18'—C19' | 1.5044 (18) |
C19—C20 | 1.379 (2) | C19'—C20' | 1.385 (2) |
C20—H20 | 0.9500 | C20'—H20' | 0.9500 |
C20—C21 | 1.386 (2) | C20'—C21' | 1.381 (2) |
C21—H21 | 0.9500 | C21'—H21' | 0.9500 |
C21—C22 | 1.373 (3) | C21'—C22' | 1.373 (2) |
C22—H22 | 0.9500 | C22'—H22' | 0.9500 |
C22—C23 | 1.379 (2) | C22'—C23' | 1.375 (2) |
C23—H23 | 0.9500 | C23'—H23' | 0.9500 |
C4—O1—C17 | 116.13 (10) | C4'—O1'—C17' | 116.94 (10) |
C14—O2—C16 | 110.36 (10) | C14'—O2'—C16' | 110.32 (11) |
N5—N1—H1 | 121.4 (10) | N5'—N1'—H1' | 120.9 (11) |
C1—N1—H1 | 119.6 (10) | C1'—N1'—H1' | 119.2 (11) |
C1—N1—N5 | 118.97 (11) | C1'—N1'—N5' | 118.22 (11) |
C4—N2—C1 | 113.68 (11) | C4'—N2'—C1' | 113.60 (11) |
C4—N3—C3 | 115.31 (11) | C4'—N3'—C3' | 115.79 (11) |
C3—N4—C13 | 122.94 (11) | C3'—N4'—C13' | 122.64 (11) |
C3—N4—C15 | 122.16 (11) | C3'—N4'—C15' | 121.38 (11) |
C13—N4—C15 | 113.03 (11) | C13'—N4'—C15' | 112.53 (11) |
C5—N5—N1 | 116.67 (11) | C5'—N5'—N1' | 116.79 (11) |
C23—N6—C19 | 117.29 (13) | C23'—N6'—C19' | 117.19 (13) |
N1—C1—C2 | 123.00 (12) | N1'—C1'—C2' | 121.93 (11) |
N2—C1—N1 | 113.80 (11) | N2'—C1'—N1' | 114.52 (11) |
N2—C1—C2 | 123.20 (12) | N2'—C1'—C2' | 123.54 (11) |
C1—C2—H2 | 121.8 | C1'—C2'—H2' | 121.8 |
C1—C2—C3 | 116.44 (12) | C1'—C2'—C3' | 116.33 (11) |
C3—C2—H2 | 121.8 | C3'—C2'—H2' | 121.8 |
N3—C3—N4 | 115.19 (11) | N3'—C3'—N4' | 115.02 (11) |
N3—C3—C2 | 121.56 (12) | N3'—C3'—C2' | 121.34 (11) |
N4—C3—C2 | 123.24 (12) | N4'—C3'—C2' | 123.61 (12) |
N2—C4—O1 | 112.42 (11) | N2'—C4'—O1' | 112.95 (11) |
N3—C4—O1 | 117.91 (11) | N3'—C4'—O1' | 117.81 (11) |
N3—C4—N2 | 129.66 (12) | N3'—C4'—N2' | 129.24 (11) |
N5—C5—H5 | 119.6 | N5'—C5'—H5' | 119.9 |
N5—C5—C6 | 120.74 (12) | N5'—C5'—C6' | 120.24 (13) |
C6—C5—H5 | 119.6 | C6'—C5'—H5' | 119.9 |
C7—C6—C5 | 119.00 (12) | C7'—C6'—C5' | 118.75 (13) |
C7—C6—C11 | 118.76 (12) | C7'—C6'—C11' | 119.07 (12) |
C11—C6—C5 | 122.21 (12) | C11'—C6'—C5' | 122.18 (12) |
C6—C7—H7 | 119.1 | C6'—C7'—H7' | 119.4 |
C8—C7—C6 | 121.80 (12) | C6'—C7'—C8' | 121.10 (14) |
C8—C7—H7 | 119.1 | C8'—C7'—H7' | 119.4 |
C7—C8—C12 | 120.45 (12) | C7'—C8'—C12' | 120.20 (14) |
C9—C8—C7 | 118.39 (12) | C9'—C8'—C7' | 118.34 (13) |
C9—C8—C12 | 121.11 (12) | C9'—C8'—C12' | 121.46 (13) |
C8—C9—H9 | 119.9 | C8'—C9'—H9' | 119.4 |
C10—C9—C8 | 120.28 (12) | C10'—C9'—C8' | 121.20 (13) |
C10—C9—H9 | 119.9 | C10'—C9'—H9' | 119.4 |
C9—C10—H10 | 119.3 | C9'—C10'—H10' | 119.8 |
C11—C10—C9 | 121.41 (12) | C9'—C10'—C11' | 120.37 (14) |
C11—C10—H10 | 119.3 | C11'—C10'—H10' | 119.8 |
C6—C11—H11 | 120.4 | C6'—C11'—H11' | 120.0 |
C10—C11—C6 | 119.26 (12) | C10'—C11'—C6' | 119.91 (13) |
C10—C11—H11 | 120.4 | C10'—C11'—H11' | 120.0 |
C8—C12—H12A | 109.5 | C8'—C12'—H12D | 109.5 |
C8—C12—H12B | 109.5 | C8'—C12'—H12E | 109.5 |
C8—C12—H12C | 109.5 | C8'—C12'—H12F | 109.5 |
H12A—C12—H12B | 109.5 | H12D—C12'—H12E | 109.5 |
H12A—C12—H12C | 109.5 | H12D—C12'—H12F | 109.5 |
H12B—C12—H12C | 109.5 | H12E—C12'—H12F | 109.5 |
N4—C13—H13A | 110.0 | N4'—C13'—H13C | 109.9 |
N4—C13—H13B | 110.0 | N4'—C13'—H13D | 109.9 |
N4—C13—C14 | 108.63 (11) | N4'—C13'—C14' | 108.83 (11) |
H13A—C13—H13B | 108.3 | H13C—C13'—H13D | 108.3 |
C14—C13—H13A | 110.0 | C14'—C13'—H13C | 109.9 |
C14—C13—H13B | 110.0 | C14'—C13'—H13D | 109.9 |
O2—C14—C13 | 112.48 (12) | O2'—C14'—C13' | 112.23 (13) |
O2—C14—H14A | 109.1 | O2'—C14'—H14C | 109.2 |
O2—C14—H14B | 109.1 | O2'—C14'—H14D | 109.2 |
C13—C14—H14A | 109.1 | C13'—C14'—H14C | 109.2 |
C13—C14—H14B | 109.1 | C13'—C14'—H14D | 109.2 |
H14A—C14—H14B | 107.8 | H14C—C14'—H14D | 107.9 |
N4—C15—H15A | 109.6 | N4'—C15'—H15C | 109.8 |
N4—C15—H15B | 109.6 | N4'—C15'—H15D | 109.8 |
N4—C15—C16 | 110.33 (12) | N4'—C15'—C16' | 109.59 (12) |
H15A—C15—H15B | 108.1 | H15C—C15'—H15D | 108.2 |
C16—C15—H15A | 109.6 | C16'—C15'—H15C | 109.8 |
C16—C15—H15B | 109.6 | C16'—C15'—H15D | 109.8 |
O2—C16—C15 | 111.14 (11) | O2'—C16'—C15' | 111.32 (12) |
O2—C16—H16A | 109.4 | O2'—C16'—H16C | 109.4 |
O2—C16—H16B | 109.4 | O2'—C16'—H16D | 109.4 |
C15—C16—H16A | 109.4 | C15'—C16'—H16C | 109.4 |
C15—C16—H16B | 109.4 | C15'—C16'—H16D | 109.4 |
H16A—C16—H16B | 108.0 | H16C—C16'—H16D | 108.0 |
O1—C17—H17A | 110.4 | O1'—C17'—H17C | 109.3 |
O1—C17—H17B | 110.4 | O1'—C17'—H17D | 109.3 |
O1—C17—C18 | 106.76 (10) | O1'—C17'—C18' | 111.53 (11) |
H17A—C17—H17B | 108.6 | H17C—C17'—H17D | 108.0 |
C18—C17—H17A | 110.4 | C18'—C17'—H17C | 109.3 |
C18—C17—H17B | 110.4 | C18'—C17'—H17D | 109.3 |
C17—C18—H18A | 109.7 | C17'—C18'—H18C | 109.5 |
C17—C18—H18B | 109.7 | C17'—C18'—H18D | 109.5 |
H18A—C18—H18B | 108.2 | H18C—C18'—H18D | 108.0 |
C19—C18—C17 | 109.76 (11) | C19'—C18'—C17' | 110.93 (11) |
C19—C18—H18A | 109.7 | C19'—C18'—H18C | 109.5 |
C19—C18—H18B | 109.7 | C19'—C18'—H18D | 109.5 |
N6—C19—C18 | 115.92 (12) | N6'—C19'—C18' | 116.42 (12) |
N6—C19—C20 | 122.47 (13) | N6'—C19'—C20' | 121.94 (13) |
C20—C19—C18 | 121.57 (13) | C20'—C19'—C18' | 121.62 (12) |
C19—C20—H20 | 120.4 | C19'—C20'—H20' | 120.2 |
C19—C20—C21 | 119.29 (15) | C21'—C20'—C19' | 119.64 (14) |
C21—C20—H20 | 120.4 | C21'—C20'—H20' | 120.2 |
C20—C21—H21 | 120.6 | C20'—C21'—H21' | 120.6 |
C22—C21—C20 | 118.82 (15) | C22'—C21'—C20' | 118.70 (14) |
C22—C21—H21 | 120.6 | C22'—C21'—H21' | 120.6 |
C21—C22—H22 | 120.7 | C21'—C22'—H22' | 120.9 |
C21—C22—C23 | 118.60 (14) | C21'—C22'—C23' | 118.23 (14) |
C23—C22—H22 | 120.7 | C23'—C22'—H22' | 120.9 |
N6—C23—C22 | 123.52 (15) | N6'—C23'—C22' | 124.28 (14) |
N6—C23—H23 | 118.2 | N6'—C23'—H23' | 117.9 |
C22—C23—H23 | 118.2 | C22'—C23'—H23' | 117.9 |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···N2′ | 0.91 (1) | 2.16 (1) | 3.0626 (16) | 169 (1) |
N1′—H1′···N2 | 0.92 (1) | 2.10 (1) | 3.0129 (16) | 178 (2) |
Acknowledgements
The authors would like to thank Judith M. White, Julie Dyall, Elizabeth A. Nelson, Gene G. Olinger Jr and Lisa Dewald at the University of Virginia and at the National Institute of Allergy and Infectious Diseases for leading the research that led to the discovery of the discrepancy. The authors would also like to thank the intramural research program at the National Center for Advancing Translational Studies for funding and the UCSD crystallography facility for the X-ray data collection.
Funding information
Funding for this research was provided by: The National Institutes of Health, National Center for Advancing Translational Sciences intramural research fundhttps://doi.org/10.13039/100006108.
References
Bruker (2013). SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Bruker (2014). APEX2 and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Cai, X., Xu, Y., Cheung, A. K., Tomlinson, R. C., Alcázar-Román, A., Murphy, L., Billich, A., Zhang, B., Feng, Y., Klumpp, M., Rondeau, J., Fazal, A. N., Wilson, C. J., Myer, C., Joberty, G., Bouwmeester, T., Labow, M. A., Finan, P. M., Porter, J. A., Ploegh, H. L., Baird, D., De Camilli, P., Tallarico, J. A. & Huang, Q. (2013). Chem. Biol. 20, 912–921. CrossRef CAS PubMed Google Scholar
Cunningham, J. (2016). Patent WO 2016112072 A1. Google Scholar
Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339–341. Web of Science CrossRef CAS IUCr Journals Google Scholar
Lichenstein, H., Rothberg, J. M., Beeharry, N., Beckett, P., Landrette, S. & Conrad, C. (2016). Patent WO2016118709. Google Scholar
Ono, M., Sun, L., Przewloka, T., Zhang, S., Kostik, E., Ying, W., Wasa, Y., Koyo, K., Wu, Y., Zhou, D. & Tatsuta, N. (2003). Patent WO 2003047516 A2. Google Scholar
Sheldrick, G. M. (2015a). Acta Cryst. A71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
Sheldrick, G. M. (2015a). Acta Cryst. C71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
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