SMTL ID : 7yhn.1

ANTI-TUMOR AGENT Y48 IN COMPLEX WITH TUBULIN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-2-2-1-mer

Ligands

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

GTP.1: 24 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, I.16, 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, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.2 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.11, A:A.12, A:D.98, A:A.99, A:A.100, A:N.101, A:S.140, A:G.144, A:T.145, A:T.145, A:G.146, A:N.206, A:N.228, A:N.228 pi-Cation interactions: A:Y.224 Salt bridges: B:K.252 GTP.8: 25 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, I.16, 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.9 27 PLIP interactions: 22 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:Q.11, C:Q.11, C:A.12, C:A.99, C:A.100, C:N.101, 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:Y.224, C:N.228, C:N.228 Water bridges: C:E.71, C:E.71, D:K.252, D:K.252, D:K.252, D:K.252 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252 GTP.11: 20 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, G.96, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, S.176, E.181, N.204, L.207, Y.222, N.226 Ligands: MG.12 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:A.97, D:G.98, D:N.99, D:S.138, D:G.141, D:G.142, D:T.143, 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 pi-Stacking: D:Y.222, D:Y.222

6 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.3: 4 residues within 4Å: Chain A: D.39, T.41, G.44, 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 MG.7: 2 residues within 4Å: Chain C: N.249, E.254 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:N.249, C:E.254, H2O.1, H2O.1 MG.9: 4 residues within 4Å: Chain C: Q.11, D.69, E.71 Ligands: GTP.8 No protein-ligand interaction detected (PLIP) MG.10: 5 residues within 4Å: Chain C: D.39, T.41, G.44, D.47, E.55 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.39, C:D.39, C:T.41, C:E.55, C:E.55 MG.12: 3 residues within 4Å: Chain D: Q.11, D.67 Ligands: GTP.11 No protein-ligand interaction detected (PLIP)

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

GDP.4: 17 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, S.138, G.140, G.141, G.142, T.143, G.144, P.171, V.175, D.177, E.181, N.204, Y.222, N.226 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:Q.11, 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:N.204, B:N.204, B:Y.222, B:N.226, B:N.226 Water bridges: B:G.141, B:G.141 pi-Stacking: B:Y.222

1 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:P.160 Salt bridges: B:D.197, B:R.251

2 x IUK: 4-methyl-3-[(4-methylphenyl)sulfonylamino]-~{N}-[(6-methylpyridin-3-yl)methyl]benzamide(Non-covalent)

IUK.6: 25 residues within 4Å: Chain A: N.101, T.179, V.181 Chain B: N.165, E.198, Y.200, V.236, C.239, L.240, N.247, D.249, L.250, K.252, L.253, N.256, M.257, T.312, V.313, A.314, A.315, I.316, N.348, K.350, T.351, A.352 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.240, B:L.240, B:L.253, B:L.253, B:N.256, B:I.316, B:K.350, B:K.350, B:A.352, A:V.181 Hydrogen bonds: B:N.247, A:N.101 IUK.13: 21 residues within 4Å: Chain C: T.179, V.181 Chain D: N.165, E.198, Y.200, V.236, C.239, L.240, D.249, L.250, L.253, N.256, M.257, V.313, A.314, A.315, I.316, N.348, K.350, T.351, A.352 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.240, D:L.240, D:L.253, D:L.253, D:N.256, D:A.314, D:I.316, D:K.350, D:K.350, D:A.352, C:V.181 Hydrogen bonds: D:N.256

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, S. et al., Optimization of Benzamide Derivatives as Potent and Orally Active Tubulin Inhibitors Targeting the Colchicine Binding Site. J.Med.Chem. (2022)

Release Date

2023-07-26

Peptides

Tubulin alpha-1B chain: AC
Tubulin beta chain: BD
Stathmin: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

Tubulin alpha-1B chain

Tubulin beta chain

Stathmin

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