- 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)
- 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)
- 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)
- 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
AC
CB
BD
DE
EF
F
- 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)
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 11 x GOL: GLYCEROL(Non-functional Binders)
- 3 x CA: CALCIUM ION(Non-covalent)
- 2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)
- 1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)
- 1 x 97O: 6,7,8-trimethoxy-1-(4-methoxyphenyl)-4,5-dihydro-2~{H}-benzo[e]indazole(Covalent)
- 3 x IMD: IMIDAZOLE(Non-covalent)
- 1 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Covalent)
- 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
AC
CB
BD
DE
EF
F