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

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ISSN: 2414-3146

1-{3-[(7-Fluoro-9H-pyrimido[4,5-b]indol-4-yl)(meth­yl)amino]­piperidin-1-yl}propan-1-one

CROSSMARK_Color_square_no_text.svg

aInstitute of Pharmaceutical Sciences, Department of Pharmaceutical and Medicinal Chemistry, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany, and bDepartment of Organic Chemistry, Johannes Gutenberg Universität Mainz, Duesbergweg 10-14, 55099 Mainz, Germany
*Correspondence e-mail: pierre.koch@uni-tuebingen.de

Edited by M. Bolte, Goethe-Universität Frankfurt, Germany (Received 5 February 2021; accepted 9 February 2021; online 23 February 2021)

The title compound, C19H22FN5O, has been synthesized as an inhibitor of glycogen synthase kinase-3β. Two mol­ecules inter­act via two N—H⋯N hydrogen bonds, forming centrosymmetric dimers.

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

Structure description

The title compound, Fig. 1[link], was synthesized by amide coupling of 7-fluoro-N-methyl-N-(piperidin-3-yl)-9H-pyrimido[4,5-b]indol-4-amine and propionic acid and inhibits the glycogen synthase kinase-3β in the low micromolar range (Andreev et al., 2020[Andreev, S., Pantsar, T., El-Gokha, A., Ansideri, F., Kudolo, M., Anton, D. B., Sita, G., Romasco, J., Geibel, C., Lämmerhofer, M., Goettert, M. I., Tarozzi, A., Laufer, S. A. & Koch, P. (2020). Int. J. Mol. Sci. 21, 7823.]). The central 13-membered ring is nearly planar with a maximum deviation of 0.137 (2) Å while the piperidine ring has a chair conformation. Two mol­ecules form centrosymmetric dimers connected by two N—H⋯N hydrogen bonds (Table 1[link]) while a three-dimensional network is formed via C—H⋯O and C—H⋯F hydrogen bonds (Table 1[link], Fig. 2[link]).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1⋯N12i 0.88 1.99 2.849 (3) 164
C5—H5⋯O23ii 0.95 2.47 3.380 (3) 161
C11—H11⋯O23iii 0.95 2.54 3.482 (3) 174
C19—H19A⋯O23 0.99 2.37 2.764 (3) 103
C19—H19A⋯F1iv 0.99 2.49 3.246 (3) 133
Symmetry codes: (i) [-x, -y+1, -z+1]; (ii) [-x+1, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]; (iii) [x-{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+1]; (iv) [-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}].
[Figure 1]
Figure 1
Perspective view of the title compound. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2]
Figure 2
Partial packing diagram of the title compound, view along the a axis. Hydrogen bonds are indicated with dashed lines. Only hydrogen atoms involved in hydrogen bonds are shown.

Synthesis and crystallization

The title compound was synthesized according to Andreev et al. (2020[Andreev, S., Pantsar, T., El-Gokha, A., Ansideri, F., Kudolo, M., Anton, D. B., Sita, G., Romasco, J., Geibel, C., Lämmerhofer, M., Goettert, M. I., Tarozzi, A., Laufer, S. A. & Koch, P. (2020). Int. J. Mol. Sci. 21, 7823.]). Crystals for the X-ray analysis precipitated from a solution of the title compound in DMSO-d6 at 298 K.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link].

Table 2
Experimental details

Crystal data
Chemical formula C19H22FN5O
Mr 355.41
Crystal system, space group Orthorhombic, Pbca
Temperature (K) 120
a, b, c (Å) 10.6982 (3), 19.8473 (8), 16.7642 (6)
V3) 3559.5 (2)
Z 8
Radiation type Mo Kα
μ (mm−1) 0.09
Crystal size (mm) 0.35 × 0.17 × 0.08
 
Data collection
Diffractometer Stoe IPDS 2T
No. of measured, independent and observed [I > 2σ(I)] reflections 9882, 4202, 2840
Rint 0.066
(sin θ/λ)max−1) 0.658
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.069, 0.194, 1.14
No. of reflections 4202
No. of parameters 237
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.36, −0.41
Computer programs: X-AREA WinXpose, Recipe and X-AREA Integrate (Stoe & Cie, 2019[Stoe & Cie (2019). X-RED32 and X-AREA. Stoe & Cie, Darmstadt, Germany.]), SHELXT2014 (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]) and SHELXL2018/3 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]).

Structural data


Computing details top

Data collection: X-AREA WinXpose (Stoe & Cie, 2019); cell refinement: X-AREA Recipe (Stoe & Cie, 2019); data reduction: X-AREA Integrate (Stoe & Cie, 2019); program(s) used to solve structure: SHELXT2014 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015b).

1-{3-[(7-Fluoro-9H-pyrimido[4,5-b]indol-4-yl)(methyl)amino]piperidin-1-yl}propan-1-one top
Crystal data top
C19H22FN5ODx = 1.326 Mg m3
Mr = 355.41Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, PbcaCell parameters from 7975 reflections
a = 10.6982 (3) Åθ = 2.4–28.3°
b = 19.8473 (8) ŵ = 0.09 mm1
c = 16.7642 (6) ÅT = 120 K
V = 3559.5 (2) Å3Block, colourless
Z = 80.35 × 0.17 × 0.08 mm
F(000) = 1504
Data collection top
Stoe IPDS 2T
diffractometer
2840 reflections with I > 2σ(I)
Radiation source: sealed X-ray tube, 12 x 0.4 mm long-fine focusRint = 0.066
Detector resolution: 6.67 pixels mm-1θmax = 27.9°, θmin = 2.4°
rotation method, ω scansh = 1412
9882 measured reflectionsk = 2226
4202 independent reflectionsl = 1922
Refinement top
Refinement on F2Primary atom site location: dual
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.069H-atom parameters constrained
wR(F2) = 0.194 w = 1/[σ2(Fo2) + (0.0822P)2 + 2.3561P]
where P = (Fo2 + 2Fc2)/3
S = 1.14(Δ/σ)max = 0.001
4202 reflectionsΔρmax = 0.36 e Å3
237 parametersΔρmin = 0.41 e Å3
0 restraints
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. H atoms found in a difference map. Then, they were positioned geometrically and refined using a riding model with C—H = 0.95 Å and Uiso(H) = 1.2Ueq(C) for aromatic CH, C—H = 0.99 Å and Uiso(H) = 1.2Ueq(C) for CH2, C—H = 1.00 Å and Uiso(H) = 1.2Ueq(C) for tertiary H and with C—H = 0.98 Å and Uiso(H) = 1.5Ueq(C) for CH3. The methyl groups were allowed to rotate but not to tip.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
F10.03835 (15)0.75389 (8)0.26711 (10)0.0344 (4)
N10.0797 (2)0.56013 (11)0.43722 (12)0.0247 (5)
H10.0115060.5621020.4665030.030*
C20.1147 (2)0.60634 (12)0.38014 (14)0.0224 (5)
C30.0481 (2)0.66282 (13)0.35527 (14)0.0243 (5)
H30.0281610.6760630.3796520.029*
C40.1002 (2)0.69815 (13)0.29309 (15)0.0260 (5)
C50.2099 (3)0.67981 (13)0.25432 (16)0.0272 (5)
H50.2393940.7052030.2101370.033*
C60.2757 (2)0.62393 (13)0.28097 (15)0.0259 (5)
H60.3510840.6109250.2553110.031*
C70.2302 (2)0.58663 (12)0.34613 (14)0.0221 (5)
C80.2673 (2)0.52527 (12)0.38809 (14)0.0213 (5)
C90.3654 (2)0.47773 (12)0.38893 (14)0.0218 (5)
N100.3530 (2)0.42059 (11)0.43277 (13)0.0255 (5)
C110.2515 (2)0.41287 (13)0.47767 (15)0.0256 (5)
H110.2458450.3718940.5067350.031*
N120.15664 (19)0.45588 (11)0.48670 (12)0.0250 (5)
C130.1679 (2)0.51100 (13)0.44078 (14)0.0230 (5)
N140.47433 (18)0.48402 (10)0.34654 (12)0.0225 (4)
C150.5310 (2)0.54981 (13)0.33467 (16)0.0283 (6)
H15A0.6127760.5510500.3609840.042*
H15B0.4768820.5846310.3575780.042*
H15C0.5415950.5581150.2774410.042*
C160.5572 (2)0.42482 (13)0.34154 (15)0.0252 (5)
H160.5030950.3838430.3381290.030*
C170.6387 (3)0.42663 (14)0.26687 (16)0.0289 (6)
H17A0.6919160.4674320.2675260.035*
H17B0.5851360.4283880.2187520.035*
C180.7214 (3)0.36317 (14)0.26433 (16)0.0308 (6)
H18A0.6681710.3229080.2564900.037*
H18B0.7797530.3662470.2186340.037*
C190.7956 (2)0.35565 (14)0.34126 (15)0.0291 (6)
H19A0.8429580.3128180.3400200.035*
H19B0.8562820.3930900.3457910.035*
N200.7121 (2)0.35610 (11)0.41082 (13)0.0275 (5)
C210.6384 (2)0.41798 (13)0.41636 (15)0.0272 (6)
H21A0.6948250.4573410.4209760.033*
H21B0.5847200.4164960.4644140.033*
C220.6811 (2)0.29723 (13)0.44725 (15)0.0261 (5)
O230.72866 (19)0.24321 (10)0.42863 (11)0.0328 (5)
C240.5879 (3)0.30135 (14)0.51579 (16)0.0317 (6)
H24A0.6105970.3398690.5504100.038*
H24B0.5036850.3102560.4937270.038*
C250.5829 (3)0.23828 (16)0.56585 (18)0.0421 (8)
H25A0.5543500.2004740.5329420.063*
H25B0.5246240.2449550.6102710.063*
H25C0.6663670.2284120.5868760.063*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
F10.0314 (8)0.0340 (9)0.0379 (9)0.0069 (7)0.0044 (7)0.0117 (7)
N10.0215 (10)0.0274 (11)0.0252 (10)0.0027 (9)0.0058 (8)0.0051 (8)
C20.0205 (11)0.0266 (13)0.0202 (11)0.0000 (10)0.0010 (9)0.0013 (9)
C30.0201 (11)0.0290 (13)0.0238 (12)0.0001 (10)0.0015 (10)0.0001 (10)
C40.0242 (12)0.0254 (13)0.0285 (12)0.0026 (10)0.0004 (10)0.0052 (10)
C50.0257 (13)0.0279 (13)0.0279 (13)0.0023 (11)0.0026 (10)0.0062 (10)
C60.0198 (12)0.0311 (14)0.0267 (12)0.0010 (10)0.0048 (10)0.0042 (10)
C70.0200 (11)0.0243 (12)0.0220 (11)0.0020 (9)0.0009 (9)0.0014 (9)
C80.0177 (11)0.0255 (12)0.0207 (11)0.0003 (9)0.0004 (9)0.0011 (9)
C90.0181 (11)0.0262 (12)0.0210 (11)0.0019 (10)0.0000 (9)0.0005 (9)
N100.0202 (10)0.0286 (11)0.0276 (11)0.0000 (9)0.0027 (8)0.0040 (8)
C110.0209 (11)0.0300 (14)0.0260 (12)0.0015 (10)0.0013 (10)0.0048 (10)
N120.0215 (10)0.0268 (11)0.0268 (11)0.0005 (9)0.0029 (8)0.0049 (8)
C130.0176 (11)0.0293 (14)0.0220 (12)0.0016 (10)0.0005 (9)0.0004 (9)
N140.0174 (10)0.0234 (11)0.0266 (10)0.0002 (8)0.0038 (8)0.0002 (8)
C150.0212 (12)0.0285 (14)0.0352 (14)0.0009 (10)0.0026 (11)0.0026 (11)
C160.0204 (12)0.0285 (13)0.0266 (12)0.0023 (10)0.0032 (10)0.0004 (10)
C170.0276 (13)0.0321 (14)0.0269 (13)0.0036 (11)0.0057 (11)0.0041 (10)
C180.0299 (14)0.0337 (15)0.0288 (13)0.0047 (12)0.0072 (11)0.0003 (11)
C190.0244 (12)0.0332 (14)0.0299 (13)0.0020 (11)0.0075 (10)0.0008 (11)
N200.0242 (11)0.0306 (12)0.0277 (11)0.0049 (9)0.0029 (9)0.0007 (9)
C210.0241 (12)0.0295 (14)0.0279 (13)0.0018 (10)0.0003 (10)0.0004 (10)
C220.0239 (12)0.0298 (14)0.0246 (12)0.0007 (10)0.0011 (10)0.0006 (10)
O230.0362 (11)0.0302 (10)0.0320 (10)0.0063 (9)0.0065 (8)0.0003 (8)
C240.0318 (14)0.0364 (15)0.0270 (13)0.0003 (12)0.0057 (11)0.0014 (11)
C250.0496 (19)0.0461 (19)0.0305 (15)0.0016 (15)0.0114 (13)0.0051 (13)
Geometric parameters (Å, º) top
F1—C41.361 (3)C15—H15C0.9800
N1—C131.359 (3)C16—C171.526 (3)
N1—C21.377 (3)C16—C211.532 (4)
N1—H10.8800C16—H161.0000
C2—C31.392 (3)C17—C181.540 (4)
C2—C71.417 (3)C17—H17A0.9900
C3—C41.375 (3)C17—H17B0.9900
C3—H30.9500C18—C191.522 (4)
C4—C51.389 (4)C18—H18A0.9900
C5—C61.388 (4)C18—H18B0.9900
C5—H50.9500C19—N201.469 (3)
C6—C71.406 (3)C19—H19A0.9900
C6—H60.9500C19—H19B0.9900
C7—C81.461 (3)N20—C221.360 (3)
C8—C131.411 (3)N20—C211.462 (3)
C8—C91.411 (3)C21—H21A0.9900
C9—N101.358 (3)C21—H21B0.9900
C9—N141.370 (3)C22—O231.227 (3)
N10—C111.330 (3)C22—C241.523 (4)
C11—N121.335 (3)C24—C251.508 (4)
C11—H110.9500C24—H24A0.9900
N12—C131.343 (3)C24—H24B0.9900
N14—C151.453 (3)C25—H25A0.9800
N14—C161.474 (3)C25—H25B0.9800
C15—H15A0.9800C25—H25C0.9800
C15—H15B0.9800
C13—N1—C2108.6 (2)C17—C16—C21110.5 (2)
C13—N1—H1125.7N14—C16—H16107.6
C2—N1—H1125.7C17—C16—H16107.6
N1—C2—C3127.3 (2)C21—C16—H16107.6
N1—C2—C7109.4 (2)C16—C17—C18109.4 (2)
C3—C2—C7123.2 (2)C16—C17—H17A109.8
C4—C3—C2115.5 (2)C18—C17—H17A109.8
C4—C3—H3122.2C16—C17—H17B109.8
C2—C3—H3122.2C18—C17—H17B109.8
F1—C4—C3117.4 (2)H17A—C17—H17B108.2
F1—C4—C5118.3 (2)C19—C18—C17110.9 (2)
C3—C4—C5124.3 (2)C19—C18—H18A109.5
C6—C5—C4119.2 (2)C17—C18—H18A109.5
C6—C5—H5120.4C19—C18—H18B109.5
C4—C5—H5120.4C17—C18—H18B109.5
C5—C6—C7119.7 (2)H18A—C18—H18B108.1
C5—C6—H6120.1N20—C19—C18110.8 (2)
C7—C6—H6120.1N20—C19—H19A109.5
C6—C7—C2118.0 (2)C18—C19—H19A109.5
C6—C7—C8136.0 (2)N20—C19—H19B109.5
C2—C7—C8105.9 (2)C18—C19—H19B109.5
C13—C8—C9114.8 (2)H19A—C19—H19B108.1
C13—C8—C7105.3 (2)C22—N20—C21124.2 (2)
C9—C8—C7139.8 (2)C22—N20—C19120.0 (2)
N10—C9—N14116.1 (2)C21—N20—C19112.5 (2)
N10—C9—C8119.4 (2)N20—C21—C16109.1 (2)
N14—C9—C8124.5 (2)N20—C21—H21A109.9
C11—N10—C9118.8 (2)C16—C21—H21A109.9
N10—C11—N12127.7 (2)N20—C21—H21B109.9
N10—C11—H11116.2C16—C21—H21B109.9
N12—C11—H11116.2H21A—C21—H21B108.3
C11—N12—C13112.8 (2)O23—C22—N20122.4 (2)
N12—C13—N1123.2 (2)O23—C22—C24120.7 (2)
N12—C13—C8126.2 (2)N20—C22—C24116.9 (2)
N1—C13—C8110.6 (2)C25—C24—C22113.5 (2)
C9—N14—C15120.5 (2)C25—C24—H24A108.9
C9—N14—C16117.9 (2)C22—C24—H24A108.9
C15—N14—C16117.21 (19)C25—C24—H24B108.9
N14—C15—H15A109.5C22—C24—H24B108.9
N14—C15—H15B109.5H24A—C24—H24B107.7
H15A—C15—H15B109.5C24—C25—H25A109.5
N14—C15—H15C109.5C24—C25—H25B109.5
H15A—C15—H15C109.5H25A—C25—H25B109.5
H15B—C15—H15C109.5C24—C25—H25C109.5
N14—C16—C17111.8 (2)H25A—C25—H25C109.5
N14—C16—C21111.4 (2)H25B—C25—H25C109.5
C13—N1—C2—C3177.1 (2)C2—N1—C13—C82.7 (3)
C13—N1—C2—C70.5 (3)C9—C8—C13—N123.8 (4)
N1—C2—C3—C4175.6 (2)C7—C8—C13—N12174.0 (2)
C7—C2—C3—C41.7 (4)C9—C8—C13—N1178.6 (2)
C2—C3—C4—F1179.8 (2)C7—C8—C13—N13.6 (3)
C2—C3—C4—C51.7 (4)N10—C9—N14—C15146.1 (2)
F1—C4—C5—C6178.7 (2)C8—C9—N14—C1535.4 (3)
C3—C4—C5—C62.7 (4)N10—C9—N14—C169.8 (3)
C4—C5—C6—C70.4 (4)C8—C9—N14—C16168.7 (2)
C5—C6—C7—C22.7 (4)C9—N14—C16—C17154.3 (2)
C5—C6—C7—C8176.5 (3)C15—N14—C16—C1749.0 (3)
N1—C2—C7—C6173.9 (2)C9—N14—C16—C2181.5 (3)
C3—C2—C7—C63.9 (4)C15—N14—C16—C2175.2 (3)
N1—C2—C7—C81.7 (3)N14—C16—C17—C18179.1 (2)
C3—C2—C7—C8179.4 (2)C21—C16—C17—C1856.2 (3)
C6—C7—C8—C13171.2 (3)C16—C17—C18—C1954.0 (3)
C2—C7—C8—C133.1 (3)C17—C18—C19—N2054.8 (3)
C6—C7—C8—C95.8 (5)C18—C19—N20—C22101.4 (3)
C2—C7—C8—C9179.9 (3)C18—C19—N20—C2158.9 (3)
C13—C8—C9—N106.0 (3)C22—N20—C21—C1698.9 (3)
C7—C8—C9—N10170.8 (3)C19—N20—C21—C1660.4 (3)
C13—C8—C9—N14175.5 (2)N14—C16—C21—N20176.0 (2)
C7—C8—C9—N147.7 (5)C17—C16—C21—N2059.1 (3)
N14—C9—N10—C11177.4 (2)C21—N20—C22—O23164.3 (2)
C8—C9—N10—C114.0 (4)C19—N20—C22—O236.4 (4)
C9—N10—C11—N121.0 (4)C21—N20—C22—C2418.4 (4)
N10—C11—N12—C133.2 (4)C19—N20—C22—C24176.4 (2)
C11—N12—C13—N1176.8 (2)O23—C22—C24—C2511.8 (4)
C11—N12—C13—C80.6 (4)N20—C22—C24—C25165.5 (3)
C2—N1—C13—N12175.1 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···N12i0.881.992.849 (3)164
C5—H5···O23ii0.952.473.380 (3)161
C11—H11···O23iii0.952.543.482 (3)174
C19—H19A···O230.992.372.764 (3)103
C19—H19A···F1iv0.992.493.246 (3)133
Symmetry codes: (i) x, y+1, z+1; (ii) x+1, y+1/2, z+1/2; (iii) x1/2, y+1/2, z+1; (iv) x+1, y1/2, z+1/2.
 

References

First citationAndreev, S., Pantsar, T., El-Gokha, A., Ansideri, F., Kudolo, M., Anton, D. B., Sita, G., Romasco, J., Geibel, C., Lämmerhofer, M., Goettert, M. I., Tarozzi, A., Laufer, S. A. & Koch, P. (2020). Int. J. Mol. Sci. 21, 7823.  CrossRef Google Scholar
First citationSheldrick, G. M. (2015a). Acta Cryst. A71, 3–8.  Web of Science CrossRef IUCr Journals Google Scholar
First citationSheldrick, G. M. (2015b). Acta Cryst. C71, 3–8.  Web of Science CrossRef IUCr Journals Google Scholar
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