SMTL ID : 6n47.1

The structure of SB-2-204-tubulin complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 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.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.4 31 PLIP interactions: 29 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.11, A:A.12, A:Q.15, A:D.98, 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:G.146, A:V.177, A:E.183, A:N.206, A:N.206, A:N.228, A:N.228 Water bridges: A:Q.11, A:E.71, A:E.71, A:E.71, A:D.98, A:S.140, A:F.141, A:A.174, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.11: 24 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 Ligands: MG.12 24 PLIP interactions: 22 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.11, C:A.12, C:Q.15, C:A.99, 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:Q.11, C:E.71, C:E.71, C:T.145, C:T.145, D:K.252 pi-Stacking: C:Y.224 Salt bridges: D:K.252 GTP.14: 22 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, A.97, N.99, S.138, G.140, G.141, G.142, T.143, G.144, V.169, P.171, V.175, S.176, E.181, N.204, Y.222, L.225, N.226 Ligands: MG.15 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: 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:G.144, D:S.176, D:S.176, D:E.181, D:N.204, D:N.204, D:N.226, D:N.226 pi-Stacking: D:Y.222, D:Y.222

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.39, T.41, G.44, D.47, 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.7: 1 residues within 4Å: Chain B: E.111 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.111 CA.13: 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:G.44, C:E.55 CA.17: 3 residues within 4Å: Chain A: S.158, E.196 Chain E: D.42 No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: Y.161, G.162, K.163, K.164 Ligand excluded by PLIP

4 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.4: 1 residues within 4Å: Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: Q.11, D.177 Ligands: GDP.5 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Ligands: GTP.11 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain D: Q.11, E.69 Ligands: GTP.14 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.69

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

GDP.5: 20 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, I.16, 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.6 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:N.99, B:S.138, B:G.141, B:G.142, B:T.143, B:T.143, B:G.144, B:D.177, B:E.181, B:N.204, B:N.204, B:N.226, B:N.226 Water bridges: B:S.138, B:L.139, B:G.140, B:T.143, B:S.145 pi-Stacking: B:Y.222, B:Y.222

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

MES.8: 10 residues within 4Å: Chain A: W.407 Chain B: R.156, P.160, D.161, R.162, M.164, N.195, T.196, D.197, R.251 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:D.197, B:R.251 MES.9: 8 residues within 4Å: Chain B: F.294, D.295, S.296, D.304, R.306, V.333, N.337, Y.340 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.295, B:S.296 Salt bridges: B:R.306

2 x KB4: 4-(2-chloropyrido[3,2-d]pyrimidin-4-yl)-7-methoxy-3,4-dihydroquinoxalin-2(1H)-one(Non-covalent)

KB4.10: 16 residues within 4Å: Chain A: T.179 Chain B: C.239, L.240, L.246, A.248, K.252, L.253, N.256, M.257, V.313, A.314, A.315, I.316, N.348, K.350, A.352 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:N.256, B:I.316, B:K.350, B:K.350, B:A.352 Hydrogen bonds: B:N.256, A:T.179, A:T.179 KB4.16: 18 residues within 4Å: Chain C: N.101, T.179, V.181 Chain D: C.239, L.240, L.246, A.248, K.252, L.253, N.256, M.257, V.313, A.314, A.315, I.316, N.348, K.350, A.352 8 PLIP interactions: 1 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:T.179, D:N.256, D:K.350 Hydrophobic interactions: D:N.256, D:I.316, D:K.350, D:K.350, D:A.352

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

ACP.18: 20 residues within 4Å: Chain F: K.74, I.148, K.150, Q.183, K.184, Y.185, L.186, K.198, D.200, R.202, R.222, H.239, L.240, T.241, N.242, D.318, M.320, I.330, E.331, N.333 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:K.74, F:K.184, 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:T.241, F:D.318, F:D.318, F:N.333 Salt bridges: F:K.74, F:K.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arnst, K.E. et al., X-ray Crystal Structure Guided Discovery and Antitumor Efficacy of Dihydroquinoxalinone as Potent Tubulin Polymerization Inhibitors. Acs Chem.Biol. (2019)

Release Date

2019-11-13

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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