SMTL ID : 6h9b.1

1,1-Diheterocyclic Ethylenes Derived from Quinaldine and Carbazole as New Tubulin Polymerization Inhibitors: Synthesis, Metabolism, and Biological Evaluation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

hetero-2-2-1-mer

Ligands

11 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: P.168, K.387 Chain B: N.347 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.347, B:N.347 Water bridges: A:K.387 Salt bridges: A:K.387 SO4.2: 5 residues within 4Å: Chain A: V.170, R.214, P.215, Y.217 Chain B: Q.245 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.215 Water bridges: A:Y.217, A:Y.217 Salt bridges: A:R.214 SO4.5: 4 residues within 4Å: Chain B: T.221, G.223, R.276 Chain C: K.319 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.223 Salt bridges: B:R.276 SO4.6: 4 residues within 4Å: Chain B: L.217, T.218, T.219 Chain C: K.319 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain B Salt bridges: C:K.319 Hydrogen bonds: B:T.218, B:T.218, B:T.219, B:T.219 SO4.7: 4 residues within 4Å: Chain B: P.272, L.273, L.284, N.298 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.273, B:N.298 SO4.10: 3 residues within 4Å: Chain C: P.168, E.200, K.387 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.200 Salt bridges: C:K.387 SO4.13: 3 residues within 4Å: Chain C: D.204, R.208, K.297 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.208, C:K.297 SO4.14: 2 residues within 4Å: Chain D: K.19, H.227 3 PLIP interactions: 3 interactions with chain D Water bridges: D:R.276 Salt bridges: D:K.19, D:H.227 SO4.15: 5 residues within 4Å: Chain D: A.271, P.272, L.273, Q.292, N.298 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.273, D:Q.292, D:N.298 SO4.16: 3 residues within 4Å: Chain D: T.221, G.223, R.276 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.221, D:G.223 Salt bridges: D:R.276 SO4.19: 3 residues within 4Å: Chain E: H.112, A.115, R.119 2 PLIP interactions: 2 interactions with chain E Salt bridges: E:H.112, E:R.119

2 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.3: 24 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, D.62, D.91, A.92, A.93, N.94, S.133, G.136, G.137, T.138, G.139, I.164, V.170, T.172, E.176, N.199, Y.217, N.221, I.224 Chain B: K.252 Ligands: MG.4 25 PLIP interactions: 23 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:Q.11, A:A.12, A:A.92, A:N.94, A:N.94, A:S.133, A:G.137, A:T.138, A:G.139, A:V.170, A:E.176, A:N.199, A:N.199, A:N.221, A:N.221 Water bridges: A:T.138, A:T.138, A:T.172, A:T.172, B:K.252 pi-Stacking: A:Y.217, A:Y.217 Salt bridges: B:K.252 GTP.11: 23 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, D.62, D.91, A.92, A.93, N.94, S.133, G.136, G.137, T.138, G.139, I.164, V.170, T.172, E.176, N.199, Y.217, N.221, I.224 Ligands: MG.12 24 PLIP interactions: 23 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.11, C:Q.11, C:Q.11, C:A.12, C:D.91, C:A.92, C:N.94, C:N.94, C:S.133, C:G.137, C:T.138, C:G.139, C:V.170, C:E.176, C:N.199, C:N.199, C:N.221, C:N.221 Water bridges: C:D.91, C:T.138, C:T.138, D:K.252 pi-Stacking: C:Y.217, C:Y.217

2 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.4: 1 residues within 4Å: Ligands: GTP.3 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain C: Q.11, E.64 Ligands: GTP.11 No protein-ligand interaction detected (PLIP)

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.8: 18 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, S.138, G.140, G.141, G.142, T.143, G.144, V.169, P.171, V.175, D.177, E.181, N.204, Y.222, N.226 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:Q.11, B:C.12, B:S.138, B:G.142, B:T.143, B:T.143, B:G.144, B:V.175, B:E.181, B:N.204, B:N.204, B:N.226, B:N.226 Water bridges: B:S.145, B:S.145 pi-Stacking: B:Y.222, B:Y.222 GDP.17: 18 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, V.169, P.171, V.175, D.177, E.181, N.204, Y.222, N.226 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:S.138, D:G.142, D:T.143, D:T.143, D:G.144, D:V.175, D:E.181, D:N.204, D:N.204, D:N.226, D:N.226 Water bridges: D:G.13, D:N.99, D:N.99, D:S.138, D:S.145 pi-Stacking: D:Y.222, D:Y.222

2 x FWH: 9-methyl-3-[1-(2-methylquinolin-4-yl)ethenyl]carbazole(Non-covalent)

FWH.9: 26 residues within 4Å: Chain A: S.171, T.172, A.173, V.174 Chain B: V.236, C.239, L.240, L.246, A.248, D.249, K.252, L.253, N.256, M.257, T.312, V.313, A.314, T.315, I.316, N.347, N.348, V.349, K.350, T.351, A.352, I.368 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.246, B:L.246, B:A.248, B:L.253, B:N.256, B:A.314, B:I.316, B:K.350, B:K.350, B:K.350, B:A.352, A:V.174 FWH.18: 26 residues within 4Å: Chain C: S.171, T.172, A.173, V.174 Chain D: V.236, C.239, L.240, L.246, A.248, D.249, K.252, L.253, N.256, M.257, T.312, V.313, A.314, T.315, I.316, N.347, N.348, V.349, K.350, T.351, A.352, I.368 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.246, D:A.248, D:L.253, D:N.256, D:A.314, D:I.316, D:K.350, D:K.350, D:K.350, D:A.352, C:V.174

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Naret, T. et al., 1,1-Diheterocyclic Ethylenes Derived from Quinaldine and Carbazole as New Tubulin-Polymerization Inhibitors: Synthesis, Metabolism, and Biological Evaluation. J. Med. Chem. (2019)

Release Date

2018-12-19

Peptides

Tubulin alpha chain: AC
Tubulin beta chain: BD
Stathmin-4: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

Tubulin alpha chain

Tubulin beta chain

Stathmin-4

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