SMTL ID : 6a4i.1

Crystal Structure of human TDO inhibitor complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-tetramer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)(Non-covalent)

HEM.1: 23 residues within 4Å: Chain A: F.75, T.78, H.79, Y.82, L.135, M.138, F.143, S.154, G.155, F.156, F.161, R.162, W.327, H.331, M.334, V.335, M.338, L.339, G.350, Y.353, L.354 Chain B: Y.45 Ligands: 9R9.2 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:F.75, A:T.78, A:Y.82, A:Y.82, A:Y.82, A:F.143, A:F.143, A:F.156, A:F.156, A:F.161, A:F.161, A:W.327, A:W.327, A:V.335, A:M.338, A:L.339, A:L.354 Hydrogen bonds: A:G.155, A:Y.353 Salt bridges: A:R.162 pi-Stacking: A:H.79, A:H.331 Metal complexes: A:H.331 HEM.5: 22 residues within 4Å: Chain A: Y.45 Chain B: F.75, T.78, H.79, Y.82, L.135, M.138, F.143, S.154, G.155, F.156, F.161, R.162, W.327, H.331, M.334, V.335, M.338, L.339, Y.353, L.354 Ligands: 9R9.6 24 PLIP interactions: 24 interactions with chain B, Hydrophobic interactions: B:F.75, B:T.78, B:Y.82, B:Y.82, B:Y.82, B:L.135, B:F.143, B:F.143, B:F.156, B:F.156, B:F.161, B:F.161, B:W.327, B:V.335, B:V.335, B:M.338, B:L.339, B:L.354, B:L.354 Hydrogen bonds: B:G.155, B:F.156 Salt bridges: B:R.162 pi-Cation interactions: B:H.79 Metal complexes: B:H.331 HEM.8: 21 residues within 4Å: Chain C: F.75, H.79, Y.82, L.135, M.138, F.143, S.154, G.155, F.156, F.161, R.162, Y.178, W.327, H.331, M.334, V.335, M.338, Y.353, L.354 Chain D: Y.45 Ligands: 9R9.9 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:F.75, C:Y.82, C:Y.82, C:Y.82, C:F.143, C:F.143, C:F.156, C:F.161, C:F.161, C:W.327, C:V.335, C:M.338, C:L.354 Hydrogen bonds: C:Y.178 Salt bridges: C:R.162 pi-Stacking: C:H.79 Metal complexes: C:H.331 HEM.10: 18 residues within 4Å: Chain C: Y.45 Chain D: F.75, H.79, Y.82, L.135, M.138, F.143, S.154, G.155, F.156, F.161, W.327, H.331, V.335, M.338, L.339, L.354 Ligands: 9R9.11 20 PLIP interactions: 20 interactions with chain D, Hydrophobic interactions: D:F.75, D:Y.82, D:Y.82, D:Y.82, D:F.143, D:F.156, D:F.156, D:F.156, D:F.161, D:F.161, D:W.327, D:V.335, D:V.335, D:M.338, D:L.339, D:L.354 Hydrogen bonds: D:G.155, D:F.156 pi-Cation interactions: D:H.79 Metal complexes: D:H.331

4 x 9R9: 1-(6-chloro-1H-indazol-4-yl)cyclohexan-1-ol(Non-covalent)

9R9.2: 10 residues within 4Å: Chain A: F.75, H.79, L.150, A.153, S.154, G.155, H.331 Chain B: Y.45, Y.48 Ligands: HEM.1 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.79, A:G.155 pi-Stacking: A:F.75 Hydrophobic interactions: B:Y.45 9R9.6: 11 residues within 4Å: Chain A: Y.45, Y.48 Chain B: F.75, H.79, F.143, L.150, A.153, G.155, H.331, L.339 Ligands: HEM.5 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.143, B:L.339, A:Y.45 Hydrogen bonds: B:H.79, B:G.155 pi-Stacking: B:F.75 9R9.9: 9 residues within 4Å: Chain C: F.75, H.79, F.143, L.150, A.153, S.154 Chain D: Y.45, Y.48 Ligands: HEM.8 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.143, C:L.150, D:Y.45 Hydrogen bonds: C:H.79 pi-Stacking: C:F.75 9R9.11: 9 residues within 4Å: Chain C: Y.45, Y.48 Chain D: F.75, H.79, L.150, A.153, S.154, G.155 Ligands: HEM.10 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:A.153, C:Y.45 Hydrogen bonds: D:H.79, D:G.155 pi-Stacking: D:F.75

3 x TRP: TRYPTOPHAN(Non-covalent)

TRP.3: 11 residues within 4Å: Chain A: V.105, R.106, E.108, W.211, R.214, T.215, P.216, I.298, R.306, F.307, P.310 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.211, A:I.298, A:F.307, A:P.310 Hydrogen bonds: A:E.108, A:W.211 Salt bridges: A:R.106, A:R.214 TRP.7: 9 residues within 4Å: Chain B: V.105, R.106, E.108, W.211, R.214, T.215, P.216, R.306, P.310 10 PLIP interactions: 9 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:W.211, B:T.215, B:P.216, B:P.310 Hydrogen bonds: B:V.105, B:E.108, B:W.211, W.7 Salt bridges: B:R.106, B:R.214 TRP.12: 11 residues within 4Å: Chain D: V.105, R.106, E.108, W.211, R.214, T.215, P.216, I.298, R.306, F.307, P.310 9 PLIP interactions: 9 interactions with chain D, Hydrophobic interactions: D:W.211, D:P.216, D:I.298, D:F.307, D:P.310 Hydrogen bonds: D:E.108, D:W.211 Salt bridges: D:R.106, D:R.214

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.4: 4 residues within 4Å: Chain A: K.113, R.117 Chain B: K.68, H.70 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Salt bridges: A:K.113, A:R.117 Hydrophobic interactions: B:H.70 Hydrogen bonds: B:H.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fu, G. et al., Crystal Structure of human TDO inhibitor complex. To Be Published

Release Date

2018-07-18

Peptides

Tryptophan 2,3-dioxygenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Tryptophan 2,3-dioxygenase