SMTL ID : 6xer.1

Tubulin-RB3_SLD in complex with colchicine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-1-mer

Ligands

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

GTP.1: 24 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 Ligands: MG.2 30 PLIP interactions: 26 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:Q.15, 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:S.178, A:E.183, A:N.206, A:N.206, A:Y.224, A:N.228, A:N.228 Water bridges: A:D.69, A:T.145, B:K.252, B:K.252, B:K.252 pi-Stacking: A:Y.224 Salt bridges: B:K.252 GTP.7: 23 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, 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.8 31 PLIP interactions: 27 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:Q.11, C:Q.11, C:A.12, C:Q.15, 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:S.178, C:E.183, C:N.206, C:N.206, C:Y.224, C:N.228, C:N.228 Water bridges: C:Q.11, C:D.69, C:T.145, D:K.252, D:K.252 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252, D:K.252 GTP.9: 21 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, 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:Q.11, D:C.12, 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

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

MG.2: 3 residues within 4Å: Chain A: E.71, D.98 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Ligands: GTP.7 No protein-ligand interaction detected (PLIP)

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

SO4.3: 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 SO4.6: 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 SO4.11: 2 residues within 4Å: Chain D: T.221, R.276 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.221, D:T.221 Salt bridges: D:R.276

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

GDP.4: 18 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, L.207, Y.222, N.226 16 PLIP interactions: 16 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:G.144, B:D.177, 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 LOC: N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide(Non-covalent)

LOC.5: 20 residues within 4Å: Chain A: S.178, T.179, A.180, V.181 Chain B: C.239, L.240, L.246, A.248, D.249, K.252, L.253, N.256, M.257, T.312, V.313, A.314, I.316, N.348, K.350, A.352 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.246, B:A.248, B:K.252, B:L.253, B:K.350, B:K.350 Hydrogen bonds: A:V.181 LOC.10: 18 residues within 4Å: Chain C: T.179, A.180, V.181 Chain D: C.239, L.240, L.246, A.248, K.252, L.253, N.256, M.257, T.312, V.313, A.314, I.316, N.348, K.350, I.368 8 PLIP interactions: 1 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:V.181, D:K.350 Hydrophobic interactions: D:L.246, D:K.252, D:L.253, D:N.256, D:K.350, D:K.350

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, H. et al., Design, Synthesis, and Biological Evaluation of Stable Colchicine-Binding Site Tubulin Inhibitors 6-Aryl-2-benzoyl-pyridines as Potential Anticancer Agents. J.Med.Chem. (2021)

Release Date

2021-08-25

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