SMTL ID : 6tde.1

Tubulin-inhibitor complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

hetero-2-2-1-mer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: P.175, K.394 Chain B: N.347 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:K.394 Hydrogen bonds: B:N.347, B:N.347 SO4.4: 3 residues within 4Å: Chain B: T.221, G.223, R.276 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.223 Salt bridges: B:R.276 SO4.5: 4 residues within 4Å: Chain B: L.217, T.218, T.219 Chain C: K.326 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:K.216, B:T.218, B:T.218, B:T.219 Salt bridges: C:K.326 SO4.8: 3 residues within 4Å: Chain C: P.175, K.394 Chain D: N.347 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:N.347 Salt bridges: C:K.394 SO4.9: 3 residues within 4Å: Chain C: D.211, R.215, K.304 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.215, C:K.304 SO4.10: 3 residues within 4Å: Chain C: Y.262, D.431, V.435 No protein-ligand interaction detected (PLIP) SO4.13: 4 residues within 4Å: Chain D: P.272, L.273, Q.292, N.298 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.273, D:N.298 SO4.14: 1 residues within 4Å: Chain D: R.276 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.276 Salt bridges: D:K.19 SO4.15: 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

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

GTP.2: 25 residues within 4Å: Chain A: 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, T.179, E.183, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.3 28 PLIP interactions: 25 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.11, A:A.12, A:Q.15, A:A.99, A:A.100, A:N.101, A:S.140, A:G.144, A:T.145, A:G.146, A:S.178, A:T.179, A:E.183, A:N.206, A:N.228, A:N.228, A:N.228 Water bridges: A:Q.11, A:Q.11, A:E.71, A:G.142, A:T.145, A:T.145, B:K.252, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.11: 25 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, T.179, E.183, N.206, Y.224, N.228, I.231 Chain D: K.252 Ligands: MG.12 24 PLIP interactions: 22 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.11, C:A.12, C:Q.15, C:A.99, C:A.100, C:N.101, C:S.140, C:G.144, C:T.145, C:G.146, C:S.178, C:E.183, C:N.206, C:N.206, C:N.228, C:N.228 Water bridges: C:E.71, C:G.142, C:T.145, C:T.145, D:K.252 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: Q.11 Ligands: GTP.2 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain C: Q.11 Chain D: K.252 Ligands: GTP.11 No protein-ligand interaction detected (PLIP)

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

GDP.6: 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 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:N.99, 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.138, B:G.141, B:S.145 pi-Stacking: B:Y.222, B:Y.222 GDP.16: 17 residues within 4Å: Chain D: 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 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, 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:N.226, D:N.226 Water bridges: D:N.99, D:S.138, D:G.140 pi-Stacking: D:Y.222, D:Y.222

2 x N3Z: ~{N}-[(10~{S})-3,4,5-trimethoxy-16-methylidene-14-oxatetracyclo[9.7.0.0^{2,7}.0^{13,17}]octadeca-1(18),2,4,6,11,13(17)-hexaen-10-yl]ethanamide(Non-covalent)

N3Z.7: 18 residues within 4Å: Chain A: S.178, T.179, 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, N.348, K.350, I.368 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.246, B:L.246, B:L.253, B:N.256, B:K.350, B:K.350 Hydrogen bonds: A:T.179, A:V.181 N3Z.17: 20 residues within 4Å: Chain C: S.178, T.179, V.181 Chain D: 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.347, N.348, K.350, I.368 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.246, D:L.253, D:K.350, D:K.350 Hydrogen bonds: C:V.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shchegravina, E.S. et al., Discovery of dihydrofuranoallocolchicinoids - Highly potent antimitotic agents with low acute toxicity. Eur.J.Med.Chem. (2020)

Release Date

2020-09-02

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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