SMTL ID : 6nng.1

Tubulin-RB3_SLD-TTL in complex with compound DJ95

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

3 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.142, G.143, G.144, T.145, G.146, I.171, V.177, S.178, E.183, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.2 26 PLIP interactions: 23 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:Q.11, A:A.12, 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:N.206, A:Y.224, A:N.228 Water bridges: A:S.140, A:F.141, B:K.252, B:K.252 pi-Stacking: A:Y.224 Salt bridges: B:K.252 GTP.9: 25 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, S.178, T.179, E.183, N.206, Y.224, N.228, I.231 Chain D: K.252 Ligands: MG.10 30 PLIP interactions: 5 interactions with chain D, 25 interactions with chain C Water bridges: D:K.252, D:K.252, D:K.252, D:K.252, C:G.13, C:D.98, C:F.141 Salt bridges: D:K.252 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.144, C:T.145, C:T.145, C:G.146, C:V.177, C:E.183, C:N.206, C:N.206, C:N.206, C:Y.224, C:N.228 pi-Stacking: C:Y.224, C:Y.224 GTP.12: 20 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, V.169, V.175, S.176, E.181, N.204, L.207, Y.222, N.226 23 PLIP interactions: 23 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:Q.11, D:C.12, D:A.97, 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:N.204, D:Y.222, D:N.226 Water bridges: D:G.13, D:S.138, D:G.141 pi-Stacking: D:Y.222, D:Y.222

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.71 Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: Q.11, D.177 Ligands: GDP.4 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain C: E.71 Chain D: K.252 Ligands: GTP.9 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain F: K.74, E.331, N.333 Ligands: ACP.14 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.331

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 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:T.41, A:G.44, A:E.55, H2O.1 CA.11: 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:D.39, C:T.41, C:E.55, H2O.11

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

GDP.4: 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.5 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, 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:N.204, B:Y.222, B:N.226 Water bridges: B:G.13, B:D.67, B:L.139, B:G.141, B:T.143, B:S.145, B:D.177 pi-Stacking: B:Y.222, B:Y.222

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

MES.6: 9 residues within 4Å: Chain B: R.156, P.160, D.161, R.162, I.163, N.195, T.196, D.197, R.251 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.156, B:R.162 Salt bridges: B:D.197, B:R.251 MES.7: 7 residues within 4Å: Chain B: F.294, D.295, S.296, D.304, R.306, N.337, Y.340 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.296, B:S.296 Salt bridges: B:R.306

1 x DJ9: 2-(1H-indol-6-yl)-4-(3,4,5-trimethoxyphenyl)-1H-imidazo[4,5-c]pyridine(Covalent)

DJ9.8: 20 residues within 4Å: Chain A: T.179, A.180, V.181 Chain B: V.236, C.239, L.240, L.246, A.248, D.249, L.250, K.252, L.253, N.256, M.257, I.316, N.347, N.348, K.350, A.352, I.368 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.252, B:L.253, B:L.253, B:N.256, B:K.350, B:K.350 Hydrogen bonds: B:D.249, B:N.256, B:K.350 Water bridges: B:N.347, A:A.180 pi-Cation interactions: B:K.350

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

ACP.14: 19 residues within 4Å: Chain F: K.74, I.148, 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 Ligands: MG.13 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:K.74, F:Q.183, F:L.186, F:K.198, F:D.200, F:R.202, F:R.222, F:R.222, F:T.241, F:T.241, F:N.242, F:N.333 Salt bridges: F:K.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arnst, K.E. et al., Colchicine Binding Site Agent DJ95 Overcomes Drug Resistance and Exhibits Antitumor Efficacy. Mol.Pharmacol. (2019)

Release Date

2019-07-10

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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