SMTL ID : 7ttf.1

Tubulin-RB3_SLD in complex with compound 12k

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-1-mer

Ligands

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

GTP.1: 25 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, I.16, D.69, 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 Ligands: GOL.9 27 PLIP interactions: 26 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.11, A:A.12, A:Q.15, A:D.69, A:D.98, A:A.99, A:A.100, A:N.101, A:N.101, A:S.140, 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 Water bridges: A:S.140, A:G.142, A:A.174 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.10: 24 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, S.178, E.183, N.206, Y.224, N.228, I.231 Chain D: K.252 Ligands: MG.11 34 PLIP interactions: 30 interactions with chain C, 4 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: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 Water bridges: C:E.71, C:D.98, C:S.140, C:A.174, D:K.252, D:K.252, D:K.252 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252 GTP.12: 21 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, G.96, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, V.169, P.171, V.175, S.176, E.181, N.204, Y.222, N.226 27 PLIP interactions: 27 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:A.97, D:G.98, 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 Water bridges: D:G.13, D:D.67, D:E.69, D:L.139, D:S.145, D:S.145, D:S.176 pi-Stacking: D:Y.222, D:Y.222

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

SO4.2: 2 residues within 4Å: Chain A: 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 SO4.3: 8 residues within 4Å: Chain A: A.314, C.315, F.343, P.348, G.350, F.351, K.352 Chain E: E.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.315, A:G.350 Salt bridges: A:K.352 SO4.6: 3 residues within 4Å: Chain B: T.221, 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 SO4.7: 8 residues within 4Å: Chain B: R.156, V.193, E.194, N.195, T.196, D.197, P.261, H.264 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.196 Salt bridges: B:R.156, B:H.264 SO4.8: 5 residues within 4Å: Chain B: K.216, L.217, T.218, T.219 Chain C: K.326 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Salt bridges: C:K.326 Hydrogen bonds: B:L.217, B:T.218, B:T.219 SO4.14: 3 residues within 4Å: Chain D: T.221, G.223, R.276 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.221 Water bridges: D:G.223, D:G.223 Salt bridges: D:R.276 SO4.15: 4 residues within 4Å: Chain D: K.19, 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

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

GDP.4: 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 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: 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:D.177, B:E.181, B:N.204, B:N.204, B:Y.222, B:N.226, B:N.226 Water bridges: B:D.67, B:S.138, B:L.139, B:T.143, B:S.145, B:S.145 pi-Stacking: B:Y.222, B:Y.222

2 x JV9: 7-methoxy-4-[2-(methylamino)-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-yl]-3,4-dihydroquinoxalin-2(1H)-one(Non-covalent)

JV9.5: 19 residues within 4Å: Chain A: T.179, V.181 Chain B: V.236, C.239, L.240, L.246, A.248, K.252, L.253, N.256, M.257, T.312, V.313, A.314, A.315, I.316, N.348, K.350, A.352 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.246, B:N.256, B:A.314, B:I.316, B:K.350, B:A.352 Hydrogen bonds: B:V.236, A:T.179 Water bridges: B:C.239, A:T.179 JV9.13: 18 residues within 4Å: Chain C: T.179 Chain D: V.236, C.239, L.240, L.246, A.248, K.252, L.253, N.256, M.257, V.313, A.314, A.315, I.316, N.348, K.350, T.351, A.352 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.246, D:N.256, D:A.314, D:I.316, D:K.350, D:A.352 Hydrogen bonds: D:V.236, C:T.179 Water bridges: D:C.239

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain A: Q.11, N.101, T.179 Chain B: K.252 Ligands: GTP.1 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.11, A:N.101, A:T.179, B:K.252, B:K.252 Water bridges: A:D.98, A:E.183, A:E.183

1 x MG: MAGNESIUM ION(Non-covalent)

MG.11: 4 residues within 4Å: Chain C: Q.11, D.69, E.71 Ligands: GTP.10 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

Related Entries With Identical Sequence