organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2414-3146

Apilimod

CROSSMARK_Color_square_no_text.svg

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

Edited by M. Zeller, Purdue University, USA (Received 21 April 2017; accepted 9 May 2017; online 23 May 2017)

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.

3D view (loading...)
[Scheme 3D1]
Chemical scheme
[Scheme 1]

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[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.]). 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[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.]). 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[Cunningham, J. (2016). Patent WO 2016112072 A1.]; Lichenstein et al. 2016[Lichenstein, H., Rothberg, J. M., Beeharry, N., Beckett, P., Landrette, S. & Conrad, C. (2016). Patent WO2016118709.]). 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[link]). 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[link]). 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.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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)
[Figure 1]
Figure 1
The mol­ecular structure of the title compound, showing 50% probability displacement ellipsoids

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[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.]). 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[link] and 3[link]). 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.

[Figure 2]
Figure 2
The 1H NMR spectrum of the title compound in deuterated chloro­form. Note the clear splitting of the morphiline peaks at 3.78 and 3.64 p.p.m..
[Figure 3]
Figure 3
13C NMR spectrum of the title compound in deuterated chloro­form

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 refinement details are summarized in Table 2[link].

Table 2
Experimental details

Crystal data
Chemical formula C23H26N6O2
Mr 418.50
Crystal system, space group Monoclinic, P21/c
Temperature (K) 100
a, b, c (Å) 14.9353 (5), 15.0367 (5), 19.4231 (7)
β (°) 98.130 (2)
V3) 4318.2 (3)
Z 8
Radiation type Cu Kα
μ (mm−1) 0.69
Crystal size (mm) 0.25 × 0.21 × 0.19
 
Data collection
Diffractometer Bruker X8 APEXII
Absorption correction Multi-scan (SADABS; Bruker, 2014[Bruker (2014). APEX2 and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.228, 0.320
No. of measured, independent and observed [I > 2σ(I)] reflections 50098, 7881, 6816
Rint 0.038
(sin θ/λ)max−1) 0.604
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.038, 0.103, 1.04
No. of reflections 7881
No. of parameters 569
No. of restraints 2
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.29, −0.22
Computer programs: APEX2 and SAINT (Bruker, 2013[Bruker (2013). SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXT (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL (Sheldrick, 2015b[Sheldrick, G. M. (2015a). Acta Cryst. C71, 3-8.]) and OLEX2 (Dolomanov et al., 2009[Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339-341.]).

Structural data


Computing details top

Data collection: APEX2 (Bruker, 2014); cell refinement: 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).

N-[(E)-(3-Methylbenzylidene)amino]-6-(morpholin-4-yl)-2-[2-(pyridin-2-yl)ethoxy]pyrimidin-4-amine top
Crystal data top
C23H26N6O2F(000) = 1776
Mr = 418.50Dx = 1.287 Mg m3
Monoclinic, P21/cCu Kα radiation, λ = 1.54178 Å
a = 14.9353 (5) ÅCell parameters from 9651 reflections
b = 15.0367 (5) Åθ = 4.2–68.5°
c = 19.4231 (7) ŵ = 0.69 mm1
β = 98.130 (2)°T = 100 K
V = 4318.2 (3) Å3Block, colourless
Z = 80.25 × 0.21 × 0.19 mm
Data collection top
Bruker X8 APEXII
diffractometer
7881 independent reflections
Radiation source: Micro Focus Rotating Anode, Bruker Microstar FR-5926816 reflections with I > 2σ(I)
Double Bounce Multilayer Mirrors monochromatorRint = 0.038
Detector resolution: 7.9 pixels mm-1θmax = 68.5°, θmin = 3.0°
ω and φ scansh = 1718
Absorption correction: multi-scan
(SADABS; Bruker, 2014)
k = 1817
Tmin = 0.228, Tmax = 0.320l = 2322
50098 measured reflections
Refinement top
Refinement on F2Primary atom site location: dual
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.038Hydrogen site location: mixed
wR(F2) = 0.103H 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 parametersΔρmax = 0.29 e Å3
2 restraintsΔρmin = 0.22 e Å3
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.34895 (6)0.49264 (6)0.73640 (4)0.0263 (2)
O20.79885 (6)0.64234 (7)0.75289 (5)0.0313 (2)
N10.35964 (8)0.58848 (8)0.51765 (6)0.0277 (2)
H10.2990 (9)0.5779 (11)0.5100 (8)0.031 (4)*
N20.35530 (7)0.54354 (7)0.62910 (5)0.0247 (2)
N30.48892 (7)0.53447 (7)0.71298 (5)0.0240 (2)
N40.62723 (8)0.58340 (8)0.68986 (6)0.0301 (3)
N50.40438 (7)0.62175 (7)0.46652 (5)0.0255 (2)
N60.41499 (8)0.34602 (8)0.92805 (6)0.0325 (3)
C10.40704 (9)0.57268 (9)0.58201 (6)0.0242 (3)
C20.49980 (9)0.58574 (9)0.59747 (7)0.0263 (3)
H20.53490.60600.56340.032*
C30.53853 (9)0.56760 (9)0.66551 (7)0.0245 (3)
C40.40211 (9)0.52482 (8)0.69093 (6)0.0232 (3)
C50.35753 (9)0.63339 (9)0.40663 (7)0.0256 (3)
H50.29470.62000.40010.031*
C60.39974 (9)0.66702 (9)0.34817 (6)0.0241 (3)
C70.34625 (9)0.67965 (9)0.28399 (7)0.0250 (3)
H70.28290.66980.28020.030*
C80.38319 (9)0.70632 (9)0.22533 (7)0.0262 (3)
C90.47498 (9)0.72490 (9)0.23255 (7)0.0286 (3)
H90.50140.74470.19350.034*
C100.52836 (9)0.71475 (10)0.29639 (7)0.0297 (3)
H100.59090.72900.30080.036*
C110.49266 (9)0.68427 (9)0.35387 (7)0.0262 (3)
H110.53070.67510.39680.031*
C120.32505 (10)0.71098 (10)0.15531 (7)0.0342 (3)
H12A0.34630.66720.12390.051*
H12B0.32890.77070.13580.051*
H12C0.26210.69810.16070.051*
C130.68901 (9)0.62522 (10)0.64810 (7)0.0313 (3)
H13A0.65450.65930.60960.038*
H13B0.72490.57920.62780.038*
C140.75126 (10)0.68681 (10)0.69423 (7)0.0327 (3)
H14A0.79540.71340.66670.039*
H14B0.71520.73580.71050.039*
C150.67356 (9)0.53962 (9)0.75186 (7)0.0286 (3)
H15A0.70840.48820.73810.034*
H15B0.62850.51720.78040.034*
C160.73665 (9)0.60377 (10)0.79406 (7)0.0301 (3)
H16A0.70090.65150.81240.036*
H16B0.77070.57210.83420.036*
C170.39265 (9)0.47784 (9)0.80631 (6)0.0267 (3)
H17A0.41700.53440.82740.032*
H17B0.44320.43520.80650.032*
C180.32146 (9)0.44048 (9)0.84671 (7)0.0276 (3)
H18A0.27220.48440.84740.033*
H18B0.29520.38570.82380.033*
C190.36342 (9)0.41962 (9)0.91997 (7)0.0275 (3)
C200.35200 (12)0.47483 (10)0.97472 (8)0.0402 (4)
H200.31470.52610.96730.048*
C210.39550 (14)0.45474 (12)1.04074 (8)0.0497 (4)
H210.38890.49221.07910.060*
C220.44831 (12)0.37974 (11)1.04972 (8)0.0435 (4)
H220.47860.36411.09440.052*
C230.45640 (10)0.32763 (11)0.99250 (8)0.0378 (3)
H230.49320.27590.99900.045*
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)
H2'0.00580.65970.58340.029*
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)
H5'0.23910.62540.73580.032*
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)
H7'0.25970.66430.85900.036*
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)
H9'0.04700.69490.96460.042*
C10'0.01152 (11)0.66672 (10)0.86247 (8)0.0345 (3)
H10'0.05180.66700.86370.041*
C11'0.04427 (10)0.65000 (9)0.80046 (7)0.0304 (3)
H11'0.00340.63870.75930.037*
C12'0.22766 (12)0.69882 (11)0.98798 (8)0.0401 (4)
H12D0.22580.64851.01980.060*
H12E0.21020.75341.01030.060*
H12F0.28910.70540.97650.060*
C13'0.16680 (10)0.69041 (11)0.51118 (7)0.0329 (3)
H13C0.12590.72020.54870.040*
H13D0.20150.64430.53240.040*
C14'0.23092 (10)0.75771 (11)0.47298 (8)0.0366 (3)
H14C0.26910.78340.50570.044*
H14D0.19540.80660.45610.044*
C15'0.17133 (9)0.61136 (9)0.40220 (7)0.0283 (3)
H15C0.20690.56130.41740.034*
H15D0.13300.58810.36870.034*
C16'0.23406 (10)0.68121 (10)0.36784 (7)0.0337 (3)
H16C0.19830.72850.34900.040*
H16D0.27440.65440.32850.040*
C17'0.08812 (9)0.52409 (9)0.32382 (6)0.0252 (3)
H17C0.02830.49840.32870.030*
H17D0.11910.48290.29520.030*
C18'0.07489 (10)0.61360 (9)0.28716 (7)0.0291 (3)
H18C0.03320.65060.31030.035*
H18D0.13370.64490.29070.035*
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)
H20'0.09560.62310.22070.045*
C21'0.08694 (11)0.59735 (12)0.11920 (8)0.0428 (4)
H21'0.14970.60250.10260.051*
C22'0.02636 (12)0.57763 (12)0.07445 (8)0.0411 (4)
H22'0.04600.56940.02620.049*
C23'0.06354 (11)0.57011 (12)0.10134 (8)0.0413 (4)
H23'0.10510.55580.07020.050*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0243 (5)0.0343 (5)0.0202 (4)0.0029 (4)0.0029 (3)0.0037 (4)
O20.0267 (5)0.0350 (5)0.0321 (5)0.0038 (4)0.0037 (4)0.0031 (4)
N10.0222 (6)0.0399 (7)0.0209 (5)0.0032 (5)0.0028 (4)0.0033 (5)
N20.0239 (5)0.0290 (6)0.0211 (5)0.0002 (4)0.0032 (4)0.0015 (4)
N30.0234 (5)0.0251 (6)0.0232 (5)0.0010 (4)0.0020 (4)0.0013 (4)
N40.0224 (6)0.0394 (7)0.0279 (6)0.0029 (5)0.0013 (5)0.0089 (5)
N50.0267 (6)0.0297 (6)0.0207 (5)0.0007 (5)0.0055 (4)0.0010 (4)
N60.0327 (6)0.0346 (7)0.0309 (6)0.0007 (5)0.0071 (5)0.0060 (5)
C10.0262 (7)0.0251 (6)0.0214 (6)0.0011 (5)0.0035 (5)0.0006 (5)
C20.0247 (7)0.0311 (7)0.0237 (6)0.0001 (5)0.0056 (5)0.0024 (5)
C30.0245 (6)0.0238 (6)0.0252 (6)0.0007 (5)0.0034 (5)0.0008 (5)
C40.0249 (6)0.0231 (6)0.0220 (6)0.0014 (5)0.0044 (5)0.0008 (5)
C50.0240 (6)0.0293 (7)0.0236 (6)0.0013 (5)0.0038 (5)0.0009 (5)
C60.0264 (7)0.0239 (6)0.0221 (6)0.0008 (5)0.0038 (5)0.0019 (5)
C70.0239 (6)0.0249 (7)0.0259 (6)0.0006 (5)0.0024 (5)0.0001 (5)
C80.0321 (7)0.0226 (6)0.0234 (6)0.0023 (5)0.0023 (5)0.0006 (5)
C90.0331 (7)0.0285 (7)0.0256 (7)0.0010 (6)0.0086 (5)0.0030 (5)
C100.0242 (7)0.0339 (7)0.0314 (7)0.0026 (5)0.0055 (5)0.0004 (6)
C110.0258 (7)0.0289 (7)0.0235 (6)0.0007 (5)0.0018 (5)0.0013 (5)
C120.0379 (8)0.0400 (8)0.0235 (7)0.0014 (6)0.0000 (6)0.0045 (6)
C130.0246 (7)0.0401 (8)0.0294 (7)0.0021 (6)0.0046 (5)0.0053 (6)
C140.0313 (7)0.0322 (8)0.0356 (8)0.0016 (6)0.0086 (6)0.0018 (6)
C150.0262 (7)0.0297 (7)0.0286 (7)0.0003 (5)0.0006 (5)0.0041 (5)
C160.0299 (7)0.0314 (7)0.0290 (7)0.0005 (6)0.0038 (6)0.0009 (6)
C170.0278 (7)0.0321 (7)0.0198 (6)0.0021 (5)0.0015 (5)0.0031 (5)
C180.0292 (7)0.0288 (7)0.0252 (7)0.0014 (5)0.0053 (5)0.0028 (5)
C190.0301 (7)0.0270 (7)0.0261 (7)0.0042 (5)0.0068 (5)0.0046 (5)
C200.0618 (10)0.0292 (8)0.0303 (8)0.0036 (7)0.0090 (7)0.0023 (6)
C210.0840 (13)0.0380 (9)0.0266 (8)0.0095 (9)0.0064 (8)0.0022 (7)
C220.0544 (10)0.0415 (9)0.0308 (8)0.0155 (8)0.0066 (7)0.0106 (7)
C230.0334 (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)
Geometric parameters (Å, º) top
O1—C41.3575 (15)O1'—C4'1.3549 (15)
O1—C171.4381 (15)O1'—C17'1.4486 (15)
O2—C141.4217 (17)O2'—C14'1.4204 (17)
O2—C161.4313 (17)O2'—C16'1.4289 (17)
N1—H10.911 (13)N1'—H1'0.915 (14)
N1—N51.3678 (15)N1'—N5'1.3684 (15)
N1—C11.3673 (17)N1'—C1'1.3656 (16)
N2—C11.3513 (17)N2'—C1'1.3527 (16)
N2—C41.3314 (17)N2'—C4'1.3303 (16)
N3—C31.3566 (17)N3'—C3'1.3564 (16)
N3—C41.3147 (17)N3'—C4'1.3172 (17)
N4—C31.3631 (18)N4'—C3'1.3635 (17)
N4—C131.4548 (17)N4'—C13'1.4515 (17)
N4—C151.4583 (17)N4'—C15'1.4587 (17)
N5—C51.2819 (17)N5'—C5'1.2781 (17)
N6—C191.3448 (19)N6'—C19'1.3429 (18)
N6—C231.3443 (19)N6'—C23'1.3363 (19)
C1—C21.3893 (19)C1'—C2'1.3877 (18)
C2—H20.9500C2'—H2'0.9500
C2—C31.3925 (18)C2'—C3'1.3918 (18)
C5—H50.9500C5'—H5'0.9500
C5—C61.4645 (18)C5'—C6'1.4675 (18)
C6—C71.3952 (18)C6'—C7'1.3940 (19)
C6—C111.4008 (19)C6'—C11'1.398 (2)
C7—H70.9500C7'—H7'0.9500
C7—C81.3932 (18)C7'—C8'1.404 (2)
C8—C91.387 (2)C8'—C9'1.384 (2)
C8—C121.5083 (18)C8'—C12'1.501 (2)
C9—H90.9500C9'—H9'0.9500
C9—C101.3843 (19)C9'—C10'1.381 (2)
C10—H100.9500C10'—H10'0.9500
C10—C111.3818 (19)C10'—C11'1.386 (2)
C11—H110.9500C11'—H11'0.9500
C12—H12A0.9800C12'—H12D0.9800
C12—H12B0.9800C12'—H12E0.9800
C12—H12C0.9800C12'—H12F0.9800
C13—H13A0.9900C13'—H13C0.9900
C13—H13B0.9900C13'—H13D0.9900
C13—C141.513 (2)C13'—C14'1.513 (2)
C14—H14A0.9900C14'—H14C0.9900
C14—H14B0.9900C14'—H14D0.9900
C15—H15A0.9900C15'—H15C0.9900
C15—H15B0.9900C15'—H15D0.9900
C15—C161.5071 (19)C15'—C16'1.500 (2)
C16—H16A0.9900C16'—H16C0.9900
C16—H16B0.9900C16'—H16D0.9900
C17—H17A0.9900C17'—H17C0.9900
C17—H17B0.9900C17'—H17D0.9900
C17—C181.5159 (18)C17'—C18'1.5225 (19)
C18—H18A0.9900C18'—H18C0.9900
C18—H18B0.9900C18'—H18D0.9900
C18—C191.5045 (18)C18'—C19'1.5044 (18)
C19—C201.379 (2)C19'—C20'1.385 (2)
C20—H200.9500C20'—H20'0.9500
C20—C211.386 (2)C20'—C21'1.381 (2)
C21—H210.9500C21'—H21'0.9500
C21—C221.373 (3)C21'—C22'1.373 (2)
C22—H220.9500C22'—H22'0.9500
C22—C231.379 (2)C22'—C23'1.375 (2)
C23—H230.9500C23'—H23'0.9500
C4—O1—C17116.13 (10)C4'—O1'—C17'116.94 (10)
C14—O2—C16110.36 (10)C14'—O2'—C16'110.32 (11)
N5—N1—H1121.4 (10)N5'—N1'—H1'120.9 (11)
C1—N1—H1119.6 (10)C1'—N1'—H1'119.2 (11)
C1—N1—N5118.97 (11)C1'—N1'—N5'118.22 (11)
C4—N2—C1113.68 (11)C4'—N2'—C1'113.60 (11)
C4—N3—C3115.31 (11)C4'—N3'—C3'115.79 (11)
C3—N4—C13122.94 (11)C3'—N4'—C13'122.64 (11)
C3—N4—C15122.16 (11)C3'—N4'—C15'121.38 (11)
C13—N4—C15113.03 (11)C13'—N4'—C15'112.53 (11)
C5—N5—N1116.67 (11)C5'—N5'—N1'116.79 (11)
C23—N6—C19117.29 (13)C23'—N6'—C19'117.19 (13)
N1—C1—C2123.00 (12)N1'—C1'—C2'121.93 (11)
N2—C1—N1113.80 (11)N2'—C1'—N1'114.52 (11)
N2—C1—C2123.20 (12)N2'—C1'—C2'123.54 (11)
C1—C2—H2121.8C1'—C2'—H2'121.8
C1—C2—C3116.44 (12)C1'—C2'—C3'116.33 (11)
C3—C2—H2121.8C3'—C2'—H2'121.8
N3—C3—N4115.19 (11)N3'—C3'—N4'115.02 (11)
N3—C3—C2121.56 (12)N3'—C3'—C2'121.34 (11)
N4—C3—C2123.24 (12)N4'—C3'—C2'123.61 (12)
N2—C4—O1112.42 (11)N2'—C4'—O1'112.95 (11)
N3—C4—O1117.91 (11)N3'—C4'—O1'117.81 (11)
N3—C4—N2129.66 (12)N3'—C4'—N2'129.24 (11)
N5—C5—H5119.6N5'—C5'—H5'119.9
N5—C5—C6120.74 (12)N5'—C5'—C6'120.24 (13)
C6—C5—H5119.6C6'—C5'—H5'119.9
C7—C6—C5119.00 (12)C7'—C6'—C5'118.75 (13)
C7—C6—C11118.76 (12)C7'—C6'—C11'119.07 (12)
C11—C6—C5122.21 (12)C11'—C6'—C5'122.18 (12)
C6—C7—H7119.1C6'—C7'—H7'119.4
C8—C7—C6121.80 (12)C6'—C7'—C8'121.10 (14)
C8—C7—H7119.1C8'—C7'—H7'119.4
C7—C8—C12120.45 (12)C7'—C8'—C12'120.20 (14)
C9—C8—C7118.39 (12)C9'—C8'—C7'118.34 (13)
C9—C8—C12121.11 (12)C9'—C8'—C12'121.46 (13)
C8—C9—H9119.9C8'—C9'—H9'119.4
C10—C9—C8120.28 (12)C10'—C9'—C8'121.20 (13)
C10—C9—H9119.9C10'—C9'—H9'119.4
C9—C10—H10119.3C9'—C10'—H10'119.8
C11—C10—C9121.41 (12)C9'—C10'—C11'120.37 (14)
C11—C10—H10119.3C11'—C10'—H10'119.8
C6—C11—H11120.4C6'—C11'—H11'120.0
C10—C11—C6119.26 (12)C10'—C11'—C6'119.91 (13)
C10—C11—H11120.4C10'—C11'—H11'120.0
C8—C12—H12A109.5C8'—C12'—H12D109.5
C8—C12—H12B109.5C8'—C12'—H12E109.5
C8—C12—H12C109.5C8'—C12'—H12F109.5
H12A—C12—H12B109.5H12D—C12'—H12E109.5
H12A—C12—H12C109.5H12D—C12'—H12F109.5
H12B—C12—H12C109.5H12E—C12'—H12F109.5
N4—C13—H13A110.0N4'—C13'—H13C109.9
N4—C13—H13B110.0N4'—C13'—H13D109.9
N4—C13—C14108.63 (11)N4'—C13'—C14'108.83 (11)
H13A—C13—H13B108.3H13C—C13'—H13D108.3
C14—C13—H13A110.0C14'—C13'—H13C109.9
C14—C13—H13B110.0C14'—C13'—H13D109.9
O2—C14—C13112.48 (12)O2'—C14'—C13'112.23 (13)
O2—C14—H14A109.1O2'—C14'—H14C109.2
O2—C14—H14B109.1O2'—C14'—H14D109.2
C13—C14—H14A109.1C13'—C14'—H14C109.2
C13—C14—H14B109.1C13'—C14'—H14D109.2
H14A—C14—H14B107.8H14C—C14'—H14D107.9
N4—C15—H15A109.6N4'—C15'—H15C109.8
N4—C15—H15B109.6N4'—C15'—H15D109.8
N4—C15—C16110.33 (12)N4'—C15'—C16'109.59 (12)
H15A—C15—H15B108.1H15C—C15'—H15D108.2
C16—C15—H15A109.6C16'—C15'—H15C109.8
C16—C15—H15B109.6C16'—C15'—H15D109.8
O2—C16—C15111.14 (11)O2'—C16'—C15'111.32 (12)
O2—C16—H16A109.4O2'—C16'—H16C109.4
O2—C16—H16B109.4O2'—C16'—H16D109.4
C15—C16—H16A109.4C15'—C16'—H16C109.4
C15—C16—H16B109.4C15'—C16'—H16D109.4
H16A—C16—H16B108.0H16C—C16'—H16D108.0
O1—C17—H17A110.4O1'—C17'—H17C109.3
O1—C17—H17B110.4O1'—C17'—H17D109.3
O1—C17—C18106.76 (10)O1'—C17'—C18'111.53 (11)
H17A—C17—H17B108.6H17C—C17'—H17D108.0
C18—C17—H17A110.4C18'—C17'—H17C109.3
C18—C17—H17B110.4C18'—C17'—H17D109.3
C17—C18—H18A109.7C17'—C18'—H18C109.5
C17—C18—H18B109.7C17'—C18'—H18D109.5
H18A—C18—H18B108.2H18C—C18'—H18D108.0
C19—C18—C17109.76 (11)C19'—C18'—C17'110.93 (11)
C19—C18—H18A109.7C19'—C18'—H18C109.5
C19—C18—H18B109.7C19'—C18'—H18D109.5
N6—C19—C18115.92 (12)N6'—C19'—C18'116.42 (12)
N6—C19—C20122.47 (13)N6'—C19'—C20'121.94 (13)
C20—C19—C18121.57 (13)C20'—C19'—C18'121.62 (12)
C19—C20—H20120.4C19'—C20'—H20'120.2
C19—C20—C21119.29 (15)C21'—C20'—C19'119.64 (14)
C21—C20—H20120.4C21'—C20'—H20'120.2
C20—C21—H21120.6C20'—C21'—H21'120.6
C22—C21—C20118.82 (15)C22'—C21'—C20'118.70 (14)
C22—C21—H21120.6C22'—C21'—H21'120.6
C21—C22—H22120.7C21'—C22'—H22'120.9
C21—C22—C23118.60 (14)C21'—C22'—C23'118.23 (14)
C23—C22—H22120.7C23'—C22'—H22'120.9
N6—C23—C22123.52 (15)N6'—C23'—C22'124.28 (14)
N6—C23—H23118.2N6'—C23'—H23'117.9
C22—C23—H23118.2C22'—C23'—H23'117.9
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···N20.91 (1)2.16 (1)3.0626 (16)169 (1)
N1—H1···N20.92 (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 fund.

References

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