SMTL ID : 6x1f.1

Tubulin-RB3_SLD-TTL in complex with compound 5m

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

3 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, S.178, E.183, N.206, Y.224, N.228, I.231 Ligands: MG.3 30 PLIP interactions: 28 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:Q.15, A:D.69, A:D.98, 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:Q.11, A:G.13, A:S.140, A:F.141, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 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 28 PLIP interactions: 26 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.11, C:Q.11, C:A.12, C:Q.15, C:D.69, 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: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, C:G.13, C:F.141, D:K.252 pi-Stacking: C:Y.224 Salt bridges: D:K.252 GTP.12: 19 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, I.16, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, V.175, S.176, E.181, N.204, Y.222, N.226 22 PLIP interactions: 22 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: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, D:S.138 pi-Stacking: D:Y.222, D:Y.222

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.39, T.41, G.44, E.55 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.39, A:D.39, A:G.44, A:E.55, H2O.2 CA.10: 4 residues within 4Å: Chain C: D.39, T.41, G.44, E.55 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.39, C:T.41, C:E.55, C:E.55, H2O.6

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: 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 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain C: E.71 Ligands: GTP.9 No protein-ligand interaction detected (PLIP)

1 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, Y.222, L.225, N.226 Ligands: MG.7 23 PLIP interactions: 23 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: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:D.67, B:A.97, B:L.139, B:G.141, B:S.145

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

MES.5: 10 residues within 4Å: Chain B: R.156, P.160, D.161, R.162, I.163, M.164, N.195, T.196, D.197, R.251 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.156 Salt bridges: B:D.197, B:R.251 MES.6: 9 residues within 4Å: Chain B: F.294, D.295, S.296, D.304, P.305, R.306, Y.310, N.337, Y.340 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.294, B:S.296 Salt bridges: B:R.306

2 x Y5M: 7-methoxy-4-(2-methyl-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-yl)-3,4-dihydroquinoxalin-2(1H)-one(Non-covalent)

Y5M.8: 17 residues within 4Å: Chain A: T.179 Chain B: 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.348, K.350, A.352 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.240, B:L.246, B:A.248, B:L.253, B:N.256, B:A.314, B:I.316, B:K.350, B:A.352 Hydrogen bonds: A:T.179 Water bridges: A:T.179 Y5M.13: 15 residues within 4Å: Chain C: N.101, T.179 Chain D: C.239, L.240, A.248, K.252, L.253, N.256, M.257, A.314, A.315, I.316, N.348, K.350, A.352 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.240, D:A.248, D:L.253, D:I.316, D:A.352 Hydrogen bonds: C:T.179

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

ACP.14: 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, H.239, 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.74, F:K.150, F:Q.183, F:L.186, F:K.198, F:R.202, F:R.222, F:T.241, F:T.241, F:N.242, F:E.331, F:N.333 Salt bridges: F:K.74, F:K.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Banerjee, S. et al., X-ray Crystallography-Guided Design, Antitumor Efficacy, and QSAR Analysis of Metabolically Stable Cyclopenta-Pyrimidinyl Dihydroquinoxalinone as a Potent Tubulin Polymerization Inhibitor. J.Med.Chem. (2021)

Release Date

2021-09-22

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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