SMTL ID : 6d88.1

Tubulin-RB3_SLD-TTL in complex with compound 13f

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

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

GTP.1: 23 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, D.98, A.99, A.100, N.101, S.140, G.142, 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.3 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:A.99, 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:Q.11, A:D.69, A:T.145 pi-Stacking: A:Y.224 GTP.9: 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, T.179, E.183, N.206, Y.224, N.228, I.231 Chain D: K.252 Ligands: MG.11 22 PLIP interactions: 21 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.11, C:Q.11, C:A.12, C:D.69, C:A.99, 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:Q.11 pi-Stacking: C:Y.224 Salt bridges: D:K.252

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.39, T.41, G.44, G.45, E.55 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.39, A:D.39, A:T.41, A:G.44, A:E.55 CA.10: 4 residues within 4Å: Chain C: D.39, T.41, G.44, E.55 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.39, C:D.39, C:T.41, C:G.44, C:E.55

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.69, E.71 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: Q.11, D.177 Ligands: GDP.4 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.177, H2O.2, H2O.3 MG.11: 3 residues within 4Å: Chain C: E.71, D.98 Ligands: GTP.9 No protein-ligand interaction detected (PLIP)

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

GDP.4: 19 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 Ligands: MG.7 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:Q.15, B:S.138, B:G.142, B:T.143, B:T.143, B:T.143, B:G.144, B:V.175, B:E.181, B:N.204, B:N.204, B:Y.222, B:N.226, B:N.226 Water bridges: B:G.13, B:N.99, B:N.99, B:S.138, B:G.141, B:S.145 pi-Stacking: B:Y.222, B:Y.222 GDP.12: 21 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, D.67, A.97, N.99, S.138, G.141, G.142, T.143, G.144, V.169, P.171, V.175, S.176, E.181, N.204, L.207, Y.222, N.226 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:D.67, D:S.138, D:T.143, D:T.143, D:G.144, D:S.176, D:E.181, D:N.204, D:N.204, D:Y.222, D:N.226, D:N.226 Water bridges: D:S.138 pi-Stacking: D:Y.222, D:Y.222

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.5: 11 residues within 4Å: Chain A: W.407 Chain B: R.156, P.160, D.161, R.162, M.164, E.194, N.195, T.196, D.197, R.251 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.162 Salt bridges: B:D.197, B:R.251 MES.6: 8 residues within 4Å: Chain B: F.294, D.295, S.296, D.304, R.306, V.333, N.337, Y.340 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.294, B:S.296 Water bridges: B:K.297 Salt bridges: B:R.306

2 x G9K: [2-(1H-indol-3-yl)-1H-imidazol-4-yl](8-methoxy-1,4-benzodioxin-6-yl)methanone(Non-covalent)

G9K.8: 18 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, K.252, L.253, N.256, M.257, V.313, A.314, N.348, K.350, I.368 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.246, B:A.248, B:L.253, B:N.256, B:K.350, B:K.350 Hydrogen bonds: B:D.249, B:N.256, A:T.179 Water bridges: A:S.178, A:S.178 G9K.13: 18 residues within 4Å: Chain C: T.179, A.180, V.181 Chain D: V.236, C.239, L.240, L.246, A.248, D.249, K.252, L.253, N.256, M.257, V.313, A.314, N.348, K.350, I.368 10 PLIP interactions: 1 interactions with chain C, 9 interactions with chain D Hydrogen bonds: C:T.179, D:D.249, D:N.256 Hydrophobic interactions: D:A.248, D:L.253, D:N.256, D:A.314, D:K.350, D:K.350 Water bridges: D:N.347

1 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.14: 19 residues within 4Å: Chain F: P.95, I.148, Q.183, K.184, Y.185, L.186, K.198, D.200, R.202, R.222, H.239, L.240, T.241, N.242, D.318, M.320, I.330, E.331, N.333 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:K.184, F:L.186, F:K.198, F:D.200, F:D.200, F:R.222, F:R.222, F:T.241, F:N.242, F:E.331, F:N.333, F:N.333 Water bridges: F:R.202 pi-Stacking: F:Y.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Q. et al., Structural Modification of the 3,4,5-Trimethoxyphenyl Moiety in the Tubulin Inhibitor VERU-111 Leads to Improved Antiproliferative Activities. J. Med. Chem. (2018)

Release Date

2018-09-12

Peptides

Tubulin alpha-1B chain: AC
Tubulin beta chain: BD
Stathmin-4: E
Tubulin tyrosine ligase: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

F
F

Tubulin alpha-1B chain

Tubulin beta chain

Stathmin-4

Tubulin tyrosine ligase

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