SMTL ID : 5gon.1

Structures of a beta-lactam bridged analogue in complex with tubulin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

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

GTP.1: 26 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, T.179, E.183, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.2 26 PLIP interactions: 25 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.143, 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:N.228, A:N.228 Water bridges: A:G.13, A:E.71, A:F.141 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.17: 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.18 24 PLIP interactions: 23 interactions with chain C, 1 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:G.146, C:V.177, C:E.183, C:N.206, C:N.206, C:N.228, C:N.228 Water bridges: C:E.71, C:S.140, C:F.141 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.98 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain B: Q.11, D.177 Ligands: GDP.7 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain C: E.71, D.98 Ligands: GTP.17 No protein-ligand interaction detected (PLIP) MG.26: 3 residues within 4Å: Chain D: Q.11, D.177 Ligands: GDP.25 No protein-ligand interaction detected (PLIP) MG.29: 1 residues within 4Å: Chain F: E.331 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.331

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: N.216, P.274, V.275, L.286, A.294, N.300 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.216, A:V.275, A:V.275 GOL.4: 9 residues within 4Å: Chain A: H.309, G.310, T.382, A.383, A.385, E.386, Y.432, V.437 Chain F: R.66 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:H.309, A:T.382, A:E.386, A:E.386, F:R.66 GOL.6: 6 residues within 4Å: Chain A: S.158, K.164, K.166, E.196, D.199 Chain E: D.39 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:D.39, A:K.164, A:K.166 GOL.9: 4 residues within 4Å: Chain B: R.391 Chain C: Y.262, E.434, V.435 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:E.434, B:R.391 GOL.10: 4 residues within 4Å: Chain B: V.175, S.176, P.220, Y.222 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.176, B:P.220 Water bridges: B:Y.222 GOL.11: 10 residues within 4Å: Chain B: E.27, A.231, S.234, G.235, F.270, R.318, P.358, S.364, A.365, T.366 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.234, B:R.318, B:S.364, B:T.366 GOL.16: 5 residues within 4Å: Chain B: G.98, K.103, W.397 Chain C: T.253, T.257 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:T.257, B:K.103 GOL.19: 6 residues within 4Å: Chain C: V.177, R.221, P.222, T.223, Y.224 Chain D: Q.245 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Q.245, C:R.221, C:Y.224 GOL.20: 5 residues within 4Å: Chain C: S.287, V.288, D.322, D.327, R.373 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:V.288, C:D.322, C:D.327 Water bridges: C:S.287, C:A.289, C:D.327 GOL.21: 8 residues within 4Å: Chain C: G.162, K.163, K.164, K.166, E.196, H.197, D.199 Chain E: F.88 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.164, C:K.166, C:K.166 GOL.27: 5 residues within 4Å: Chain D: V.175, S.176, P.220, T.221, Y.222 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.176, D:Y.222 GOL.28: 8 residues within 4Å: Chain C: W.407 Chain D: R.156, P.160, D.161, R.162, D.197, R.251 Ligands: IMD.23 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.161, D:D.197, D:R.251

3 x CA: CALCIUM ION(Non-covalent)

CA.5: 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.12: 2 residues within 4Å: Chain B: E.108, E.111 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.111 CA.15: 2 residues within 4Å: Chain C: E.279, Y.282 No protein-ligand interaction detected (PLIP)

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

GDP.7: 18 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, N.226 Ligands: MG.8 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:S.138, B:G.142, B:T.143, B:T.143, B:G.144, B:V.175, B:E.181, B:N.204, B:N.204, B:N.226, B:N.226 Water bridges: B:G.13, B:L.139, B:G.141, B:G.141, B:T.143 pi-Stacking: B:Y.222, B:Y.222 GDP.25: 19 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, S.138, G.140, G.141, G.142, T.143, G.144, V.169, P.171, V.175, D.177, E.181, N.204, Y.222, N.226 Ligands: MG.26 17 PLIP interactions: 17 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:V.175, D:E.181, D:N.204, D:N.204, D:N.226, D:N.226 Water bridges: D:S.138, D:S.138 pi-Stacking: D:Y.222, D:Y.222

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

MES.13: 10 residues within 4Å: Chain A: W.407 Chain B: R.156, P.160, D.161, R.162, I.163, M.164, N.195, D.197, R.251 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Salt bridges: B:D.197, B:R.251 Water bridges: A:R.105

1 x 6ZR: (3R,4R)-4-(4-methoxy-3-oxidanyl-phenyl)-3-methyl-1-(3,4,5-trimethoxyphenyl)azetidin-2-one(Non-covalent)

6ZR.14: 21 residues within 4Å: Chain A: T.179, A.180, V.181 Chain B: G.235, V.236, C.239, L.240, L.246, A.248, D.249, K.252, L.253, N.256, M.257, A.314, A.315, I.316, N.347, K.350, T.351, A.352 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.246, B:K.252, B:L.253, B:A.314, B:K.350, B:K.350 Hydrogen bonds: B:D.249

3 x IMD: IMIDAZOLE(Non-covalent)

IMD.22: 3 residues within 4Å: Chain C: Y.262, D.431, V.435 No protein-ligand interaction detected (PLIP) IMD.23: 6 residues within 4Å: Chain C: G.410, E.411 Chain D: P.160 Chain E: R.107, L.111 Ligands: GOL.28 No protein-ligand interaction detected (PLIP) IMD.24: 5 residues within 4Å: Chain C: C.4, S.165, L.167, T.253, Q.256 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, P. et al., Potent Antitumor Activities and Structure Basis of the Chiral beta-Lactam Bridged Analogue of Combretastatin A-4 Binding to Tubulin. J. Med. Chem. (2016)

Release Date

2017-03-22

Peptides

Tubulin alpha-1B chain: AC
Tubulin beta-2B chain: BD
Stathmin-4: E
Uncharacterized protein: 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

Uncharacterized protein

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