SMTL ID : 5z4p.1

Crystal structure of tubulin-stathmin-TTL-Compound TCA complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

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

GTP.1: 25 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, T.179, E.183, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.2 25 PLIP interactions: 24 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:Q.11, A:A.12, A:Q.15, A:D.98, A:A.99, A:A.100, A:N.101, A:S.140, A:G.143, A:G.144, A:T.145, A:T.145, A:G.146, A:S.178, A:E.183, A:N.206, A:N.206, A:Y.224, A:N.228, A:N.228 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.15: 24 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, I.16, 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.16 27 PLIP interactions: 24 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Q.11, C:Q.11, C:A.12, C:Q.15, C:D.98, C:A.99, C:A.100, C:N.101, C:S.140, C:G.143, 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, D:K.252 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252, D:K.252

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.69, E.71 Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain B: Q.11, D.177 Ligands: GDP.7 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.177, H2O.1 MG.16: 3 residues within 4Å: Chain C: D.69, E.71 Ligands: GTP.15 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.71, H2O.1 MG.25: 5 residues within 4Å: Chain D: Q.11, E.69, A.97, N.99 Ligands: GDP.24 No protein-ligand interaction detected (PLIP)

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: N.216, A.273, P.274, V.275, I.276, A.294, N.300 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.275, A:V.275, A:N.300 GOL.4: 5 residues within 4Å: Chain A: H.309, T.382, A.383, E.386 Chain F: R.66 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:R.66, A:T.382, A:E.386 GOL.6: 8 residues within 4Å: Chain A: S.158, G.162, K.164, K.166, E.196, H.197, D.199 Chain E: D.88 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:K.166, A:D.199, E:D.88 GOL.9: 3 residues within 4Å: Chain B: V.175, P.220, Y.222 No protein-ligand interaction detected (PLIP) GOL.13: 5 residues within 4Å: Chain B: R.391 Chain C: Y.262, E.434, V.435 Ligands: IMD.21 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.391, B:R.391, C:E.434 GOL.14: 5 residues within 4Å: Chain B: G.98, K.103, W.397 Chain C: T.253, T.257 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.253 GOL.17: 6 residues within 4Å: Chain C: V.177, R.221, P.222, T.223, Y.224 Chain D: Q.245 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:Q.245, C:R.221, C:R.221, C:Y.224 GOL.18: 6 residues within 4Å: Chain C: S.287, V.288, D.322, V.323, D.327, R.373 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.288, C:D.322, C:D.327 GOL.19: 10 residues within 4Å: Chain C: S.158, G.162, K.163, K.164, S.165, K.166, E.196, H.197, D.199 Chain E: F.137 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.162, C:K.163, C:K.164, C:K.166, C:K.166 GOL.26: 4 residues within 4Å: Chain D: V.175, P.220, T.221, Y.222 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:P.220, D:Y.222 GOL.27: 9 residues within 4Å: Chain D: R.156, P.160, D.161, R.162, I.163, D.197, R.251 Chain E: M.163 Ligands: IMD.22 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:P.160, D:R.251, D:R.251

3 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain A: D.39, T.41, G.44, F.49, 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: 2 residues within 4Å: Chain B: E.108, E.111 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.111 CA.20: 1 residues within 4Å: Chain C: Y.282 No protein-ligand interaction detected (PLIP)

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

GDP.7: 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.8 20 PLIP interactions: 20 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:L.139, B:G.141, B:G.141 GDP.24: 23 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, I.16, E.69, A.97, N.99, S.138, G.140, G.141, G.142, T.143, G.144, V.175, D.177, E.181, N.204, L.207, Y.222, L.225, N.226 Ligands: MG.25 22 PLIP interactions: 22 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:S.138, D:G.141, D:G.142, D:T.143, D:T.143, D:T.143, D:G.144, D:V.175, D:E.181, D:N.204, D:N.204, D:Y.222, D:N.226, D:N.226 Water bridges: D:G.13, D:S.138, D:S.145 pi-Stacking: D:Y.222, D:Y.222

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

MES.11: 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 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.162 Water bridges: B:R.156 Salt bridges: B:D.197, B:R.251

1 x 97O: 6,7,8-trimethoxy-1-(4-methoxyphenyl)-4,5-dihydro-2~{H}-benzo[e]indazole(Covalent)

97O.12: 19 residues within 4Å: Chain A: T.179 Chain B: V.236, C.239, L.240, L.246, N.247, A.248, D.249, K.252, L.253, N.256, V.313, A.314, A.315, I.316, N.348, K.350, A.352, I.368 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.246, B:A.248, B:L.253, B:N.256, B:K.350, B:K.350 Hydrogen bonds: B:N.256

3 x IMD: IMIDAZOLE(Non-covalent)

IMD.21: 4 residues within 4Å: Chain C: Y.262, D.431, E.434 Ligands: GOL.13 No protein-ligand interaction detected (PLIP) IMD.22: 5 residues within 4Å: Chain C: G.410, E.411 Chain D: D.161 Chain E: R.156 Ligands: GOL.27 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.410 IMD.23: 6 residues within 4Å: Chain C: C.4, Q.133, S.165, L.167, L.242, T.253 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.165

1 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Covalent)

ACP.28: 13 residues within 4Å: Chain F: K.74, K.184, Y.185, L.186, K.198, D.200, H.239, L.240, T.241, M.320, I.330, E.331, N.333 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:K.74, F:K.184, F:L.186, F:K.198, F:E.331

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, H. et al., Discovery and Design of novel Tubulin inhibitors. To Be Published

Release Date

2019-01-16

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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