| Literature DB >> 28316827 |
Vegard Torp Lien1, Dag Erlend Olberg1, Jo Klaveness1, Carl Henrik Görbitz2.
Abstract
The protein tubulin is central for maintaining normal cellular processes, and mol-ecules inter-fering with the tubulin dynamics have potential in the treatment of cancerous diseases. The title compound, C17H14N2O5, was prepared as a lead compound in a project dedicated to the development of therapeutic agents binding to the colchicine binding site on tubulin, thereby inter-fering with the cell division in cancer cells. It holds many of the main structural characteristics for colchicine binding and has the potential for further modification and functionalization. In the title mol-ecule, the benzene ring is inclined to the quinoline ring by 76.10 (8)°. In the crystal, mol-ecules are linked by two pairs of C-H⋯O hydrogen bonds, forming tubular-like arrangements, propagating along the direction of the diagonals of the ab plane, and enclosing R22(26) and R22(16) ring motifs.Entities:
Keywords: N-substituted quinolone; crystal structure; cytotoxic agents; hydrogen bonding; tubulin polymerization
Year: 2017 PMID: 28316827 PMCID: PMC5347072 DOI: 10.1107/S2056989017002948
Source DB: PubMed Journal: Acta Crystallogr E Crystallogr Commun
Figure 1(a) Schematic drawing of two analogues of (I) in the Cambridge Structural Database (CSD, Version 5.37; Groom et al., 2016 ▸) identified by their six-letter reference codes. (b) Number of entries in the CSD retrieved by using various search fragments. The raw quinolin-4(1H)-one skeleton (with potential substituents on all C and N atoms) yields 759 hits (including a small number of duplicates). Three types of specifications and combinations thereof are then explored: introduction of bonds to O atoms (–OH, alkoxy or phenoxy) from C6 and C7, N1-substitution (blue, subset aromatic ring), and including only acyclic bonds from C2 and C3 atoms (red, X = any atom type, subset H only). Green and violet colours indicate the two molecules in (a). (c) Final CSD search fragment used in the conformational analysis. Dashed bonds have bond type ‘any’, Q is N or C, Z is ‘not hydrogen’, while T3 means the atom has three bonded atoms. The indicated torsion angle runs between the encircled atoms through the two ring centroids.
Figure 2(a) The molecular structure of (I) with some selected bond lengths (Å; s.u.’s = 0.002 Å) at 295 K. Displacement ellipsoids are shown at the 50% probability level. Pink spheres are the centroids for the two six-membered rings, and the dashed green lines defines the torsion angle discussed in the text. (b) View along the centroid–centroid vector showing the torsion angle from (a) and two neighbouring molecules A and B at (−x + 1, −y + 2, −z + 1) and (x − 1, y, z), respectively. (c) As in (b), but rotated ca 27° around the vertical axis to display two short intermolecular interactions involving the nitrophenyl substituent; H2′⋯O1(−x + 1, −y + 2, −z + 1) is 2.53 Å, while H3′⋯C4A(x − 1, y, z) is 2.72 Å.
Hydrogen-bond geometry (Å, °)
|
|
| H⋯ |
|
|
|---|---|---|---|---|
| C2′—H2′⋯O1i | 0.93 | 2.53 | 3.320 (2) | 143 |
| C10—H103⋯O1′ii | 0.96 | 2.60 | 3.512 (3) | 160 |
Symmetry codes: (i) ; (ii) .
Figure 3A viewed along the normal to (110) of the crystal packing of compound (I). Hydrogen bonds are shown as dashed lines (see Table 1 ▸). For clarity, only H atoms, H2′ and H103, have been included.
Experimental details
| Crystal data | |
| Chemical formula | C17H14N2O5 |
|
| 326.30 |
| Crystal system, space group | Monoclinic, |
| Temperature (K) | 295 |
|
| 8.3736 (4), 11.7694 (5), 15.5623 (8) |
| β (°) | 93.251 (1) |
|
| 1531.23 (13) |
|
| 4 |
| Radiation type | Mo |
| μ (mm−1) | 0.11 |
| Crystal size (mm) | 0.66 × 0.27 × 0.08 |
| Data collection | |
| Diffractometer | Bruker D8 Venture diffractometer with a Photon 100 CMOS detector |
| Absorption correction | Multi-scan ( |
|
| 0.930, 1.000 |
| No. of measured, independent and observed [ | 20516, 3142, 2298 |
|
| 0.032 |
| (sin θ/λ)max (Å−1) | 0.626 |
| Refinement | |
|
| 0.047, 0.127, 1.03 |
| No. of reflections | 3142 |
| No. of parameters | 219 |
| H-atom treatment | H-atom parameters constrained |
| Δρmax, Δρmin (e Å−3) | 0.20, −0.21 |
Computer programs: APEX3 and SAINT-Plus (Bruker, 2016 ▸), SHELXT2014 (Sheldrick, 2015a ▸), SHELXL2014 (Sheldrick, 2015b ▸) and Mercury (Macrae et al., 2008 ▸).
| C17H14N2O5 | |
| Monoclinic, | Mo |
| Cell parameters from 8925 reflections | |
| θ = 2.6–26.4° | |
| µ = 0.11 mm−1 | |
| β = 93.251 (1)° | |
| Flat lens, yellow | |
| 0.66 × 0.27 × 0.08 mm |
| Bruker D8 Venture diffractometer with a Photon 100 CMOS detector | 3142 independent reflections |
| Radiation source: fine-focus sealed tube | 2298 reflections with |
| Graphite monochromator | |
| Detector resolution: 8.3 pixels mm-1 | θmax = 26.4°, θmin = 2.2° |
| Sets of exposures each taken over 0.5° ω rotation scans | |
| Absorption correction: multi-scan (SADABS; Bruker, 2016) | |
| 20516 measured reflections |
| Refinement on | Primary atom site location: structure-invariant direct methods |
| Least-squares matrix: full | Secondary atom site location: difference Fourier map |
| Hydrogen site location: inferred from neighbouring sites | |
| H-atom parameters constrained | |
| 3142 reflections | (Δ/σ)max < 0.001 |
| 219 parameters | Δρmax = 0.20 e Å−3 |
| 0 restraints | Δρmin = −0.21 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. |
| O1 | 0.82921 (15) | 0.99910 (12) | 0.42505 (8) | 0.0623 (4) | |
| O2 | 0.86545 (15) | 0.77881 (14) | 0.70970 (8) | 0.0684 (4) | |
| O3 | 0.59678 (16) | 0.67943 (13) | 0.71853 (8) | 0.0679 (4) | |
| N1 | 0.41894 (16) | 0.81504 (12) | 0.43553 (9) | 0.0477 (4) | |
| C2 | 0.4438 (2) | 0.88507 (16) | 0.36804 (11) | 0.0528 (4) | |
| H2 | 0.3660 | 0.8887 | 0.3230 | 0.063* | |
| C3 | 0.5757 (2) | 0.94908 (16) | 0.36357 (12) | 0.0538 (5) | |
| H3 | 0.5850 | 0.9969 | 0.3165 | 0.065* | |
| C4 | 0.7020 (2) | 0.94582 (15) | 0.42906 (11) | 0.0466 (4) | |
| C5 | 0.7864 (2) | 0.86419 (15) | 0.57179 (11) | 0.0461 (4) | |
| H5 | 0.8813 | 0.9051 | 0.5704 | 0.055* | |
| C6 | 0.7612 (2) | 0.79688 (16) | 0.64091 (11) | 0.0501 (4) | |
| C7 | 0.6135 (2) | 0.73853 (16) | 0.64500 (11) | 0.0508 (4) | |
| C8 | 0.5013 (2) | 0.74416 (16) | 0.57787 (11) | 0.0491 (4) | |
| H8 | 0.4056 | 0.7045 | 0.5803 | 0.059* | |
| C9 | 1.0221 (2) | 0.8218 (2) | 0.70451 (15) | 0.0789 (7) | |
| H91 | 1.0657 | 0.7957 | 0.6523 | 0.118* | |
| H92 | 1.0879 | 0.7955 | 0.7530 | 0.118* | |
| H93 | 1.0191 | 0.9033 | 0.7047 | 0.118* | |
| C10 | 0.4431 (3) | 0.6342 (2) | 0.73209 (14) | 0.0791 (7) | |
| H101 | 0.3652 | 0.6941 | 0.7281 | 0.119* | |
| H102 | 0.4437 | 0.6002 | 0.7882 | 0.119* | |
| H103 | 0.4164 | 0.5777 | 0.6892 | 0.119* | |
| C4A | 0.67157 (18) | 0.87302 (14) | 0.50243 (10) | 0.0422 (4) | |
| C8A | 0.53089 (18) | 0.81007 (14) | 0.50514 (10) | 0.0430 (4) | |
| O1' | −0.2498 (2) | 0.57251 (18) | 0.39917 (15) | 0.1105 (7) | |
| O2' | −0.0978 (2) | 0.42948 (16) | 0.37958 (14) | 0.1038 (6) | |
| N1' | −0.1179 (2) | 0.52979 (17) | 0.39326 (12) | 0.0718 (5) | |
| C1' | 0.2824 (2) | 0.74056 (15) | 0.42899 (11) | 0.0460 (4) | |
| C2' | 0.1327 (2) | 0.78390 (16) | 0.43907 (12) | 0.0547 (5) | |
| H2' | 0.1198 | 0.8597 | 0.4540 | 0.066* | |
| C3' | 0.0017 (2) | 0.71397 (17) | 0.42679 (13) | 0.0588 (5) | |
| H3' | −0.1009 | 0.7421 | 0.4327 | 0.071* | |
| C4' | 0.0242 (2) | 0.60273 (16) | 0.40578 (12) | 0.0532 (5) | |
| C5' | 0.1729 (2) | 0.55765 (18) | 0.39643 (14) | 0.0663 (6) | |
| H5' | 0.1852 | 0.4815 | 0.3823 | 0.080* | |
| C6' | 0.3036 (2) | 0.62773 (17) | 0.40849 (14) | 0.0635 (5) | |
| H6' | 0.4060 | 0.5992 | 0.4028 | 0.076* |
| O1 | 0.0581 (8) | 0.0703 (9) | 0.0589 (8) | −0.0198 (7) | 0.0065 (6) | 0.0060 (7) |
| O2 | 0.0502 (7) | 0.0978 (11) | 0.0556 (8) | −0.0166 (7) | −0.0109 (6) | 0.0185 (7) |
| O3 | 0.0605 (8) | 0.0899 (10) | 0.0524 (8) | −0.0207 (7) | −0.0041 (6) | 0.0208 (7) |
| N1 | 0.0440 (8) | 0.0555 (9) | 0.0431 (8) | −0.0060 (7) | −0.0013 (6) | −0.0012 (7) |
| C2 | 0.0568 (10) | 0.0594 (11) | 0.0413 (10) | −0.0010 (9) | −0.0040 (8) | 0.0006 (9) |
| C3 | 0.0608 (11) | 0.0567 (11) | 0.0439 (10) | −0.0062 (9) | 0.0039 (8) | 0.0050 (8) |
| C4 | 0.0493 (10) | 0.0459 (9) | 0.0452 (10) | −0.0034 (8) | 0.0088 (7) | −0.0055 (8) |
| C5 | 0.0388 (8) | 0.0533 (10) | 0.0463 (10) | −0.0070 (7) | 0.0041 (7) | −0.0036 (8) |
| C6 | 0.0437 (9) | 0.0621 (11) | 0.0438 (10) | −0.0031 (8) | −0.0022 (7) | 0.0008 (8) |
| C7 | 0.0498 (10) | 0.0593 (11) | 0.0433 (10) | −0.0067 (8) | 0.0043 (8) | 0.0055 (8) |
| C8 | 0.0418 (9) | 0.0583 (10) | 0.0470 (10) | −0.0109 (8) | 0.0023 (7) | 0.0011 (8) |
| C9 | 0.0613 (13) | 0.0953 (17) | 0.0772 (15) | −0.0268 (12) | −0.0206 (11) | 0.0183 (13) |
| C10 | 0.0775 (14) | 0.1009 (18) | 0.0584 (13) | −0.0415 (13) | 0.0006 (10) | 0.0181 (12) |
| C4A | 0.0407 (8) | 0.0448 (9) | 0.0414 (9) | −0.0013 (7) | 0.0061 (7) | −0.0053 (7) |
| C8A | 0.0403 (9) | 0.0494 (10) | 0.0391 (9) | 0.0002 (7) | 0.0021 (7) | −0.0051 (7) |
| O1' | 0.0539 (10) | 0.1104 (14) | 0.165 (2) | −0.0167 (10) | −0.0103 (10) | −0.0218 (13) |
| O2' | 0.0966 (13) | 0.0717 (12) | 0.1419 (18) | −0.0284 (10) | −0.0051 (11) | −0.0223 (11) |
| N1' | 0.0650 (12) | 0.0740 (13) | 0.0750 (12) | −0.0178 (10) | −0.0073 (9) | −0.0091 (10) |
| C1' | 0.0446 (9) | 0.0528 (10) | 0.0402 (9) | −0.0043 (8) | −0.0018 (7) | −0.0047 (8) |
| C2' | 0.0497 (10) | 0.0523 (10) | 0.0616 (12) | 0.0017 (8) | −0.0004 (8) | −0.0110 (9) |
| C3' | 0.0430 (10) | 0.0652 (12) | 0.0681 (13) | 0.0017 (9) | 0.0013 (9) | −0.0098 (10) |
| C4' | 0.0504 (10) | 0.0596 (11) | 0.0489 (10) | −0.0094 (9) | −0.0037 (8) | −0.0077 (9) |
| C5' | 0.0638 (12) | 0.0512 (11) | 0.0842 (15) | −0.0031 (10) | 0.0050 (10) | −0.0163 (10) |
| C6' | 0.0481 (10) | 0.0614 (12) | 0.0813 (14) | 0.0039 (9) | 0.0061 (9) | −0.0145 (11) |
| O1—C4 | 1.241 (2) | C9—H91 | 0.9600 |
| O2—C6 | 1.359 (2) | C9—H92 | 0.9600 |
| O2—C9 | 1.412 (2) | C9—H93 | 0.9600 |
| O3—C7 | 1.353 (2) | C10—H101 | 0.9600 |
| O3—C10 | 1.419 (2) | C10—H102 | 0.9600 |
| N1—C2 | 1.360 (2) | C10—H103 | 0.9600 |
| N1—C8A | 1.393 (2) | C4A—C8A | 1.394 (2) |
| N1—C1' | 1.440 (2) | O1'—N1' | 1.222 (2) |
| C2—C3 | 1.342 (2) | O2'—N1' | 1.213 (2) |
| C2—H2 | 0.9300 | N1'—C4' | 1.471 (2) |
| C3—C4 | 1.427 (3) | C1'—C2' | 1.370 (2) |
| C3—H3 | 0.9300 | C1'—C6' | 1.380 (3) |
| C4—C4A | 1.461 (2) | C2'—C3' | 1.376 (3) |
| C5—C6 | 1.362 (2) | C2'—H2' | 0.9300 |
| C5—C4A | 1.408 (2) | C3'—C4' | 1.365 (3) |
| C5—H5 | 0.9300 | C3'—H3' | 0.9300 |
| C6—C7 | 1.419 (2) | C4'—C5' | 1.369 (3) |
| C7—C8 | 1.366 (2) | C5'—C6' | 1.375 (3) |
| C8—C8A | 1.406 (2) | C5'—H5' | 0.9300 |
| C8—H8 | 0.9300 | C6'—H6' | 0.9300 |
| C6—O2—C9 | 117.12 (15) | O3—C10—H102 | 109.5 |
| C7—O3—C10 | 117.17 (15) | H101—C10—H102 | 109.5 |
| C2—N1—C8A | 120.01 (14) | O3—C10—H103 | 109.5 |
| C2—N1—C1' | 118.03 (14) | H101—C10—H103 | 109.5 |
| C8A—N1—C1' | 121.74 (14) | H102—C10—H103 | 109.5 |
| C3—C2—N1 | 122.86 (16) | C8A—C4A—C5 | 118.63 (15) |
| C3—C2—H2 | 118.6 | C8A—C4A—C4 | 121.33 (15) |
| N1—C2—H2 | 118.6 | C5—C4A—C4 | 120.03 (15) |
| C2—C3—C4 | 121.77 (17) | N1—C8A—C4A | 119.12 (15) |
| C2—C3—H3 | 119.1 | N1—C8A—C8 | 120.52 (15) |
| C4—C3—H3 | 119.1 | C4A—C8A—C8 | 120.35 (15) |
| O1—C4—C3 | 123.65 (16) | O2'—N1'—O1' | 123.3 (2) |
| O1—C4—C4A | 121.58 (16) | O2'—N1'—C4' | 118.15 (19) |
| C3—C4—C4A | 114.77 (15) | O1'—N1'—C4' | 118.53 (19) |
| C6—C5—C4A | 121.24 (15) | C2'—C1'—C6' | 121.02 (17) |
| C6—C5—H5 | 119.4 | C2'—C1'—N1 | 119.55 (16) |
| C4A—C5—H5 | 119.4 | C6'—C1'—N1 | 119.35 (16) |
| O2—C6—C5 | 126.29 (16) | C1'—C2'—C3' | 119.25 (17) |
| O2—C6—C7 | 114.29 (15) | C1'—C2'—H2' | 120.4 |
| C5—C6—C7 | 119.43 (16) | C3'—C2'—H2' | 120.4 |
| O3—C7—C8 | 124.88 (16) | C4'—C3'—C2' | 119.14 (17) |
| O3—C7—C6 | 114.76 (15) | C4'—C3'—H3' | 120.4 |
| C8—C7—C6 | 120.36 (16) | C2'—C3'—H3' | 120.4 |
| C7—C8—C8A | 119.83 (16) | C3'—C4'—C5' | 122.41 (17) |
| C7—C8—H8 | 120.1 | C3'—C4'—N1' | 118.02 (17) |
| C8A—C8—H8 | 120.1 | C5'—C4'—N1' | 119.57 (18) |
| O2—C9—H91 | 109.5 | C4'—C5'—C6' | 118.35 (18) |
| O2—C9—H92 | 109.5 | C4'—C5'—H5' | 120.8 |
| H91—C9—H92 | 109.5 | C6'—C5'—H5' | 120.8 |
| O2—C9—H93 | 109.5 | C5'—C6'—C1' | 119.82 (18) |
| H91—C9—H93 | 109.5 | C5'—C6'—H6' | 120.1 |
| H92—C9—H93 | 109.5 | C1'—C6'—H6' | 120.1 |
| O3—C10—H101 | 109.5 | ||
| C8A—N1—C2—C3 | 1.9 (3) | C1'—N1—C8A—C8 | −9.9 (2) |
| C1'—N1—C2—C3 | −172.90 (17) | C5—C4A—C8A—N1 | −177.76 (15) |
| N1—C2—C3—C4 | 1.6 (3) | C4—C4A—C8A—N1 | 1.4 (2) |
| C2—C3—C4—O1 | 176.06 (18) | C5—C4A—C8A—C8 | 3.4 (2) |
| C2—C3—C4—C4A | −3.3 (3) | C4—C4A—C8A—C8 | −177.44 (15) |
| C9—O2—C6—C5 | −8.6 (3) | C7—C8—C8A—N1 | 178.84 (16) |
| C9—O2—C6—C7 | 171.73 (18) | C7—C8—C8A—C4A | −2.3 (3) |
| C4A—C5—C6—O2 | 177.51 (17) | C2—N1—C1'—C2' | −75.8 (2) |
| C4A—C5—C6—C7 | −2.9 (3) | C8A—N1—C1'—C2' | 109.47 (19) |
| C10—O3—C7—C8 | −9.8 (3) | C2—N1—C1'—C6' | 101.0 (2) |
| C10—O3—C7—C6 | 170.42 (18) | C8A—N1—C1'—C6' | −73.7 (2) |
| O2—C6—C7—O3 | 3.4 (2) | C6'—C1'—C2'—C3' | −1.3 (3) |
| C5—C6—C7—O3 | −176.25 (17) | N1—C1'—C2'—C3' | 175.48 (17) |
| O2—C6—C7—C8 | −176.36 (18) | C1'—C2'—C3'—C4' | 0.7 (3) |
| C5—C6—C7—C8 | 4.0 (3) | C2'—C3'—C4'—C5' | 0.1 (3) |
| O3—C7—C8—C8A | 178.89 (17) | C2'—C3'—C4'—N1' | 179.83 (18) |
| C6—C7—C8—C8A | −1.4 (3) | O2'—N1'—C4'—C3' | −175.7 (2) |
| C6—C5—C4A—C8A | −0.8 (2) | O1'—N1'—C4'—C3' | 2.5 (3) |
| C6—C5—C4A—C4 | −179.93 (16) | O2'—N1'—C4'—C5' | 4.1 (3) |
| O1—C4—C4A—C8A | −177.59 (16) | O1'—N1'—C4'—C5' | −177.7 (2) |
| C3—C4—C4A—C8A | 1.8 (2) | C3'—C4'—C5'—C6' | −0.2 (3) |
| O1—C4—C4A—C5 | 1.6 (2) | N1'—C4'—C5'—C6' | 179.99 (19) |
| C3—C4—C4A—C5 | −179.05 (16) | C4'—C5'—C6'—C1' | −0.4 (3) |
| C2—N1—C8A—C4A | −3.3 (2) | C2'—C1'—C6'—C5' | 1.1 (3) |
| C1'—N1—C8A—C4A | 171.27 (15) | N1—C1'—C6'—C5' | −175.66 (18) |
| C2—N1—C8A—C8 | 175.52 (16) |
| H··· | ||||
| C2′—H2′···O1i | 0.93 | 2.53 | 3.320 (2) | 143 |
| C10—H103···O1′ii | 0.96 | 2.60 | 3.512 (3) | 160 |