SMTL ID : 7ce6.1

Crystal structure of T2R-TTL-Compound9 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

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

GTP.1: 30 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, I.16, D.69, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, I.171, P.173, A.174, V.177, S.178, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 Chain B: K.252 Ligands: MG.2 27 PLIP interactions: 22 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:D.98, 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:S.178, A:N.206, A:N.206, A:N.228, A:N.228 Water bridges: A:S.140, A:F.141, B:K.252, B:K.252, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252, B:K.252 GTP.9: 30 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, I.16, D.69, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, I.171, P.173, A.174, V.177, S.178, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 Chain D: K.252 Ligands: MG.10 29 PLIP interactions: 24 interactions with chain C, 5 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:N.101, C:S.140, C:G.144, C:T.145, C:T.145, C:G.146, C:N.206, C:N.206, C:Y.224, C:N.228, C:N.228 Water bridges: C:E.71, C:S.140, C:G.142, D:K.252, D:K.252, D:K.252 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252, D:K.252 GTP.12: 27 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, I.16, A.97, G.98, N.99, S.138, G.140, G.141, G.142, T.143, G.144, V.169, P.171, S.172, V.175, S.176, E.181, N.204, L.207, Y.222, L.225, N.226, V.229 Ligands: MG.14 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:A.97, D:G.98, D:N.99, D:S.138, D:G.141, D:G.142, D:T.143, D:T.143, D:T.143, D:G.144, D:S.176, D:N.204, D:N.204, D:N.226, D:N.226 pi-Stacking: D:Y.222, D:Y.222

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: Q.11, D.98 Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain B: Q.11, D.177 Chain C: E.254 Ligands: GDP.5 No protein-ligand interaction detected (PLIP) MG.10: 6 residues within 4Å: Chain C: Q.11, D.69, E.71, D.98 Chain D: K.252 Ligands: GTP.9 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain D: Q.11, D.67, E.69 Ligands: GTP.12 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.69

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 7 residues within 4Å: Chain A: D.39, T.41, G.44, G.45, F.49, N.50, 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.11: 5 residues within 4Å: Chain C: D.39, T.41, G.44, G.45, E.55 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.39, C:T.41, C:E.55, C:E.55, H2O.6

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: N.216, A.273, P.274, V.275, I.276, L.286, A.294, N.300 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.216, A:V.275

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

GDP.5: 28 residues within 4Å: Chain B: G.10, Q.11, C.12, G.13, Q.15, I.16, A.97, S.138, G.140, G.141, G.142, T.143, G.144, S.145, V.169, P.171, S.172, V.175, S.176, D.177, E.181, N.204, L.207, Y.222, L.225, N.226, V.229 Ligands: MG.6 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:S.138, B:G.142, B:T.143, B:G.144, B:V.175, B:V.175, B:D.177, B:N.204, B:N.204, B:N.226, B:N.226 Water bridges: B:A.97, B:S.138, B:S.138, B:G.140, B:G.141, B:S.145 pi-Stacking: B:Y.222, B:Y.222

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

MES.7: 12 residues within 4Å: Chain A: W.407 Chain B: R.156, P.160, D.161, R.162, I.163, M.164, E.194, N.195, T.196, D.197, R.251 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.156 Salt bridges: B:D.197, B:R.251

2 x AF6: N-benzyl-9H-beta-carbolin-3-amine(Non-covalent)

AF6.8: 23 residues within 4Å: Chain B: I.4, Y.50, Q.134, N.165, F.167, E.198, Y.200, V.236, T.237, C.239, L.240, L.246, L.250, L.253, A.254, M.257, A.314, A.315, I.316, K.350, T.351, A.352, I.368 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:N.165, B:F.167, B:F.167, B:Y.200, B:T.237, B:L.240, B:L.246, B:L.250, B:L.253, B:L.253, B:I.316, B:I.316, B:A.352 Hydrogen bonds: B:E.198, B:Y.200 Water bridges: B:L.253 AF6.13: 23 residues within 4Å: Chain D: I.4, Y.50, Q.134, N.165, F.167, E.198, Y.200, V.236, T.237, C.239, L.240, L.246, L.250, L.253, N.256, M.257, F.266, A.314, I.316, K.350, T.351, A.352, I.368 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:F.167, D:F.167, D:Y.200, D:T.237, D:L.240, D:L.250, D:L.253, D:L.253, D:A.352, D:I.368 Hydrogen bonds: D:E.198, D:Y.200

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

ACP.15: 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, L.240, T.241, N.242, D.318, M.320, I.330, E.331, N.333 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:K.74, F:K.184, F:L.186, F:K.198, F:R.202, F:R.222, F:R.222, F:T.241, F:T.241, F:N.242, F:N.242, F:E.331, F:N.333 Salt bridges: F:K.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, J. et al., Small Molecules Promote Selective Denaturation and Degradation of Tubulin Heterodimers through a Low-Barrier Hydrogen Bond. J.Med.Chem. (2022)

Release Date

2021-06-30

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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