SMTL ID : 7tte.1

Tubulin-RB3_SLD in complex with compound 12j

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-2-2-1-mer

Ligands

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

GTP.1: 23 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, I.16, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, V.177, S.178, E.183, N.206, Y.224, N.228, I.231 Chain B: K.252 27 PLIP interactions: 26 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:Q.15, A:D.69, A:D.98, A:D.98, A:A.99, A:A.100, A:N.101, A:N.101, A:S.140, A:G.143, A:G.144, A:T.145, A:T.145, A:G.146, A:V.177, A:E.183, A:N.206, A:N.206, A:Y.224, A:N.228, A:N.228 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.6: 23 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, D.69, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, V.177, T.179, E.183, N.206, Y.224, N.228, I.231 Ligands: MG.7 27 PLIP interactions: 25 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.11, C:Q.11, C:Q.11, C:A.12, C:Q.15, C:D.69, C:D.98, C:A.99, C:A.100, C:N.101, C:N.101, C:S.140, C:G.144, C:T.145, C:T.145, C:G.146, C:V.177, C:E.183, C:N.206, C:N.206, C:Y.224, C:N.228, C:N.228 pi-Stacking: C:Y.224, C:Y.224 Water bridges: D:K.252, D:K.252 GTP.8: 22 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, G.96, A.97, G.98, N.99, S.138, G.140, G.141, G.142, T.143, G.144, V.169, P.171, V.175, S.176, E.181, N.204, Y.222, N.226 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:Q.15, D:A.97, D:N.99, D:N.99, D:S.138, D:G.142, D:T.143, D:T.143, D:G.144, D:E.181, D:N.204, D:N.204, D:Y.222, D:N.226, D:N.226 pi-Stacking: D:Y.222, D:Y.222

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

SO4.2: 3 residues within 4Å: Chain A: P.175, K.394 Chain B: N.347 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.394 Hydrogen bonds: B:N.347 SO4.5: 4 residues within 4Å: Chain B: T.221, Y.222, G.223, R.276 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.221, B:T.221, B:G.223 Salt bridges: B:R.276 SO4.10: 3 residues within 4Å: Chain D: H.227, R.276, G.277 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.277 Salt bridges: D:K.19, D:H.227 SO4.11: 2 residues within 4Å: Chain D: T.221, R.276 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.221, D:G.223 Salt bridges: D:R.276

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

GDP.3: 17 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, 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 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:S.138, B:G.142, B:T.143, B:T.143, B:T.143, B:T.143, B:G.144, B:V.175, B:D.177, B:N.204, B:N.204, B:Y.222, B:N.226, B:N.226 pi-Stacking: B:Y.222, B:Y.222

2 x JVR: 4-[2-(cyclopropylamino)-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-yl]-7-methoxy-3,4-dihydroquinoxalin-2(1H)-one(Non-covalent)

JVR.4: 13 residues within 4Å: Chain A: T.179 Chain B: C.239, L.240, L.246, A.248, L.253, N.256, M.257, A.314, I.316, N.348, K.350, A.352 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.246, B:L.253, B:A.314, B:I.316, B:K.350, B:A.352 Water bridges: B:V.236, B:C.239 Hydrogen bonds: A:T.179 JVR.9: 17 residues within 4Å: Chain C: N.101, T.179 Chain D: Y.200, V.236, L.240, A.248, D.249, L.250, K.252, L.253, N.256, M.257, V.313, A.314, I.316, N.348, K.350 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.240, D:L.250, D:L.253, D:I.316 Hydrogen bonds: D:D.249, C:T.179

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.7: 1 residues within 4Å: Ligands: GTP.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pochampally, S. et al., Design, Synthesis, and Biological Evaluation of Pyrimidine Dihydroquinoxalinone Derivatives as Tubulin Colchicine Site-Binding Agents That Displayed Potent Anticancer Activity Both In Vitro and In Vivo. Acs Pharmacol Transl Sci (2023)

Release Date

2023-04-12

Peptides

Tubulin alpha-1B 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-1B chain

Tubulin beta chain

Stathmin-4

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