SMTL ID : 8cgz.1

tubulin-AB8939 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

hetero-2-2-1-mer

Ligands

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

GTP.1: 24 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, T.179, E.183, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.2 25 PLIP interactions: 24 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:Q.15, 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:S.140 pi-Stacking: A:Y.224, 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.69, D.98, A.99, 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 Chain D: K.252 Ligands: MG.8 26 PLIP interactions: 24 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.11, C:Q.11, C:A.12, C:Q.15, 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:G.13, C:F.141, D:K.252 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.69, E.71 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain C: Q.11 Ligands: GTP.7 No protein-ligand interaction detected (PLIP)

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

GDP.3: 17 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, P.171, V.175, D.177, E.181, N.204, Y.222, N.226 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: 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: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:T.143 pi-Stacking: B:Y.222, B:Y.222 GDP.9: 17 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, P.171, V.175, S.176, E.181, N.204, Y.222, N.226 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: 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:Y.222, D:N.226, D:N.226 Water bridges: D:G.13, D:N.99, D:G.141, D:S.145 pi-Stacking: D:Y.222, D:Y.222

2 x UIY: 1-[4-[2-[[5-(ethoxymethyl)-2-methyl-phenyl]amino]-1,3-oxazol-5-yl]phenyl]imidazolidin-2-one(Non-covalent)

UIY.4: 24 residues within 4Å: Chain A: T.179, A.180, V.181 Chain B: V.236, C.239, L.240, L.246, A.248, D.249, L.250, K.252, L.253, N.256, M.257, T.312, V.313, A.314, A.315, I.316, N.347, N.348, K.350, A.352, I.368 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.240, B:L.250, B:L.253, B:L.253, B:N.256, B:K.350, B:K.350, B:A.352, B:I.368 Hydrogen bonds: B:D.249, B:D.249, B:N.347 UIY.10: 24 residues within 4Å: Chain C: T.179, A.180, V.181 Chain D: Y.200, V.236, C.239, L.240, L.246, A.248, D.249, L.250, K.252, L.253, N.256, M.257, V.313, A.314, A.315, N.347, N.348, V.349, K.350, A.352, I.368 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:L.240, D:L.246, D:L.246, D:L.250, D:L.253, D:L.253, D:L.253, D:N.256, D:A.314, D:K.350, D:K.350, D:K.350, D:I.368 Hydrogen bonds: D:D.249, D:D.249, D:N.347

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

SO4.5: 4 residues within 4Å: Chain B: T.221, G.223, D.224, R.276 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.221, B:T.221, B:G.223, B:D.224 Salt bridges: B:R.276 SO4.6: 4 residues within 4Å: Chain B: K.216, L.217, T.218, T.219 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.218, B:T.218, B:T.219 Salt bridges: C:K.326 SO4.11: 2 residues within 4Å: Chain D: T.221, R.276 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.221 Salt bridges: D:R.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Humbert, M. et al., Development of AB8939, a Novel Colchicine-like Microtubule Synthetic Destabilizer with the Ability to Overcome Multidrug Resistance. TO BE PUBLISHED

Release Date

2024-08-14

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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