SMTL ID : 7cnm.1

YDX in complex with tubulin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.44 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

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

GTP.1: 24 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, E.183, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.2 29 PLIP interactions: 3 interactions with chain B, 26 interactions with chain A Water bridges: B:K.252, B:K.252, A:Q.11, A:Q.11, A:G.13, A:F.141, A:T.145, A:T.145, A:A.174 Salt bridges: B:K.252 Hydrogen bonds: A:Q.11, A:A.12, A:Q.15, A:A.99, 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 pi-Stacking: A:Y.224, A:Y.224 GTP.9: 23 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, E.183, N.206, Y.224, N.228, I.231 Chain D: K.252 Ligands: MG.10 26 PLIP interactions: 23 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Q.11, C:A.12, C:Q.15, C:D.98, C:A.99, C:N.101, C:S.140, C:G.143, 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:G.13, C:F.141, C:T.145, C:T.145, D:K.252, D:K.252 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: Q.11, E.69 Ligands: GDP.4 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain C: D.69 Ligands: GTP.9 No protein-ligand interaction detected (PLIP)

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:D.39, 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: 5 interactions with chain C Metal complexes: C:D.39, C:T.41, C:G.44, C:E.55, C:E.55

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

GDP.4: 19 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, P.171, V.175, S.176, E.181, N.204, Y.222, N.226 Ligands: MG.5, G70.8 17 PLIP interactions: 17 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:E.181, B:N.204, B:N.204, B:N.226, B:N.226 Water bridges: B:S.138, B:L.139, B:G.141, B:T.143, B:S.145 GDP.13: 18 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, A.97, S.138, G.141, G.142, T.143, G.144, V.169, V.175, S.176, E.181, N.204, Y.222, L.225, N.226 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:S.138, D:G.141, D:G.142, D:T.143, D:T.143, D:G.144, D:E.181, D:N.204, D:N.204, D:N.226, D:N.226 Water bridges: D:G.13, D:S.145

3 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, M.164, N.195, D.197, R.251 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:D.197, B:R.251 MES.7: 8 residues within 4Å: Chain B: F.294, D.295, S.296, P.305, R.306, V.333, N.337, Y.340 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.296 Salt bridges: B:R.306 MES.12: 6 residues within 4Å: Chain C: Y.262, P.263, R.264, D.431, E.434, V.435 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.264, C:I.265, C:E.434 Salt bridges: C:D.431 pi-Cation interactions: C:Y.262

2 x G70: (2~{S},4~{S})-4-[[2-[(1~{R},3~{R})-1-acetyloxy-4-methyl-3-[[(2~{S},3~{S})-3-methyl-2-[[(2~{R})-1-methylpiperidin-2-yl]carbonylamino]pentanoyl]amino]pentyl]-1,3-thiazol-4-yl]carbonylamino]-5-cyclohexyl-2-methyl-pentanoic acid(Non-covalent)

G70.8: 17 residues within 4Å: Chain B: Q.15, K.174, V.175, D.177, P.220, T.221, Y.222, G.223, R.276 Chain C: L.248, P.325, N.329, I.332, F.351, V.353, I.355 Ligands: GDP.4 15 PLIP interactions: 8 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:Q.15, B:Y.222, B:Y.222, C:L.248, C:P.325, C:I.332, C:V.353, C:I.355 Hydrogen bonds: B:T.221, B:Y.222, B:G.223, C:N.329, C:N.329 Salt bridges: B:D.177, B:R.276 G70.14: 10 residues within 4Å: Chain D: Q.15, P.173, K.174, V.175, D.177, P.220, T.221, Y.222, G.223, R.276 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:V.175, D:Y.222 Hydrogen bonds: D:T.221, D:Y.222, D:G.223 Salt bridges: D:D.177, D:R.276

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

ACP.15: 15 residues within 4Å: Chain F: K.74, I.148, Q.183, K.184, Y.185, L.186, K.198, D.200, L.240, T.241, N.242, D.318, M.320, I.330, E.331 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:K.74, F:Q.183, F:L.186, F:K.198, F:D.200, F:T.241, F:N.242 Salt bridges: F:K.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chengyong, W. et al., The high-resolution X-ray structure of vinca-domain inhibitors of microtubules provides a rational approach for drug design. Febs Lett. (2021)

Release Date

2021-08-04

Peptides

Tubulin alpha-1B chain: AC
Tubulin beta 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 chain

Stathmin-4

Tubulin tyrosine ligase

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