SMTL ID : 5osk.1

Tubulin-7j complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.11 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.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 Ligands: MG.2 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:Q.15, A:D.98, A:A.99, A:N.101, A:N.101, A:S.140, A:G.144, A:T.145, A:G.146, A:V.177, A:E.183, A:N.206, A:N.206, A:N.228, A:N.228 Water bridges: A:G.13, A:D.98, A:T.145, A:T.145, A:E.183 pi-Stacking: A:Y.224 GTP.12: 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.13 27 PLIP interactions: 24 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Q.11, C:A.12, C:Q.15, C:A.99, C:N.101, C:S.140, C:G.144, C:T.145, C:G.146, C:V.177, C:E.183, C:N.206, C:N.206, C:N.228, C:N.228 Water bridges: C:G.13, C:E.71, C:F.141, C:T.145, C:T.145, C:T.179, C:E.183, D:K.252, D:K.252 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252

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

MG.2: 1 residues within 4Å: Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: Q.11, D.177 Ligands: GDP.6 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Ligands: GTP.12 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain D: Q.11 Ligands: GDP.19 No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain F: E.331, N.333 Ligands: ACP.22 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.331

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: N.216, P.274, V.275, A.294, N.300 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.216, A:V.275, A:N.300, A:N.300 GOL.4: 5 residues within 4Å: Chain A: D.160, Y.161, G.162, K.163, K.164 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.162, A:K.163, A:K.164 GOL.5: 6 residues within 4Å: Chain A: V.177, R.221, P.222, T.223, Y.224 Chain B: Q.245 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.245, A:Y.224, A:Y.224 GOL.8: 3 residues within 4Å: Chain B: R.391 Chain C: Y.262, V.435 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.391, B:R.391 GOL.9: 4 residues within 4Å: Chain B: V.175, P.220, T.221, Y.222 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.222 Water bridges: B:D.177 GOL.14: 4 residues within 4Å: Chain C: V.177, R.221, T.223, Y.224 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.221, C:R.221, C:Y.224 Water bridges: C:T.223, C:T.225 GOL.16: 7 residues within 4Å: Chain C: K.163, K.164, K.166, E.196, H.197, D.199 Chain E: F.91 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.166, C:K.166, C:K.166 Water bridges: C:K.164

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, P.171, V.175, D.177, E.181, N.204, Y.222, N.226 Ligands: MG.7 22 PLIP interactions: 22 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:G.144, B:V.175, B:N.204, B:N.204, B:N.226, B:N.226 Water bridges: B:S.138, B:G.140, B:G.141, B:T.143, B:S.145, B:D.177, B:D.177 pi-Stacking: B:Y.222, B:Y.222 GDP.19: 18 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, V.169, P.171, S.176, E.181, N.204, Y.222, N.226 Ligands: MG.20 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, 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:G.13, D:G.140, D:G.141, D:S.145

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

MES.10: 9 residues within 4Å: Chain A: W.407 Chain B: R.156, P.160, D.161, R.162, M.164, N.195, D.197, R.251 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.156, B:R.251 Salt bridges: B:D.197, B:R.251

1 x A9Q: 3-(2,5-Dimethoxybenzyl)-7-sulfamoyloxy-6-methoxy-3,4-dihydroquinazolin-2(1H)-one(Non-covalent)

A9Q.11: 23 residues within 4Å: Chain A: S.178, T.179, A.180, 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.347, N.348, V.349, K.350, A.352 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.246, B:L.253, B:N.256, B:I.316, B:K.350 Hydrogen bonds: B:N.256, B:N.347, B:N.347, A:S.178, A:T.179 Salt bridges: B:K.350

1 x CA: CALCIUM ION(Non-covalent)

CA.15: 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

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.17: 1 residues within 4Å: Chain C: D.431 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.431 pi-Stacking: C:Y.262 IMD.18: 5 residues within 4Å: Chain C: Q.133, S.165, L.167, L.242, T.253 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.165, C:S.165

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

ACP.22: 19 residues within 4Å: Chain F: K.74, I.148, K.150, Q.183, K.184, Y.185, L.186, K.198, D.200, R.202, R.222, L.240, T.241, D.318, M.320, I.330, E.331, N.333 Ligands: MG.21 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:K.74, F:K.184, F:L.186, F:K.198, F:D.200, F:R.202, F:R.222, F:R.222, F:T.241, F:T.241, F:T.241, F:D.318, F:D.318, F:D.318, F:E.331, F:N.333 Salt bridges: F:K.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dohle, W. et al., Quinazolinone-Based Anticancer Agents: Synthesis, Antiproliferative SAR, Antitubulin Activity, and Tubulin Co-crystal Structure. J. Med. Chem. (2018)

Release Date

2017-12-20

Peptides

Tubulin alpha-1B chain: AC
Tubulin beta-2B 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-2B chain

Stathmin-4

Tubulin-Tyrosine Ligase

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