SMTL ID : 6vbn.1

Crystal Structure of hTDO2 bound to inhibitor GNE1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.18 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 21 residues within 4Å: Chain A: F.58, H.62, Y.65, F.69, L.118, F.126, S.137, G.138, F.139, F.144, R.145, W.310, H.314, V.318, M.321, L.322, T.328, Y.336, L.337 Chain B: Y.28 Ligands: QVY.2 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:F.58, A:Y.65, A:Y.65, A:Y.65, A:F.69, A:L.118, A:F.126, A:F.126, A:F.139, A:F.144, A:W.310, A:W.310, A:M.321, A:L.337, A:L.337 Hydrogen bonds: A:G.138, A:T.328 Salt bridges: A:R.145 Metal complexes: A:H.314 HEM.3: 22 residues within 4Å: Chain A: Y.28 Chain B: F.58, H.62, Y.65, F.69, L.118, F.126, S.137, G.138, F.139, F.144, R.145, W.310, H.314, M.317, V.318, M.321, L.322, T.328, Y.336, L.337 Ligands: QVY.4 23 PLIP interactions: 23 interactions with chain B, Hydrophobic interactions: B:F.58, B:Y.65, B:Y.65, B:Y.65, B:F.69, B:L.118, B:F.126, B:F.139, B:F.144, B:W.310, B:W.310, B:V.318, B:M.321, B:L.322, B:L.322, B:L.337, B:L.337 Hydrogen bonds: B:G.138, B:T.328, B:Y.336 Salt bridges: B:R.145 pi-Stacking: B:H.314 Metal complexes: B:H.314 HEM.5: 22 residues within 4Å: Chain C: F.58, H.62, Y.65, F.69, L.118, F.126, S.137, G.138, F.139, F.144, R.145, W.310, H.314, M.317, V.318, M.321, L.322, T.328, Y.336, L.337 Chain D: Y.28 Ligands: QVY.7 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:F.58, C:Y.65, C:Y.65, C:Y.65, C:F.69, C:L.118, C:F.126, C:F.126, C:F.139, C:F.144, C:W.310, C:W.310, C:V.318, C:L.322, C:L.337, C:L.337 Hydrogen bonds: C:G.138, C:T.328, C:T.328, C:Y.336 Salt bridges: C:R.145 Metal complexes: C:H.314 HEM.8: 22 residues within 4Å: Chain C: Y.28 Chain D: F.58, H.62, Y.65, F.69, L.118, F.126, S.137, G.138, F.139, F.144, R.145, W.310, H.314, M.317, V.318, M.321, L.322, T.328, Y.336, L.337 Ligands: QVY.6 21 PLIP interactions: 21 interactions with chain D, Hydrophobic interactions: D:F.58, D:Y.65, D:Y.65, D:Y.65, D:F.69, D:L.118, D:F.126, D:F.126, D:F.139, D:F.144, D:W.310, D:W.310, D:M.321, D:L.322, D:L.337, D:L.337 Hydrogen bonds: D:G.138, D:T.328 Salt bridges: D:R.145 pi-Stacking: D:H.314 Metal complexes: D:H.314

4 x QVY: 1,5-anhydro-2,3-dideoxy-3-[(5S)-5H-imidazo[5,1-a]isoindol-5-yl]-D-threo-pentitol(Non-covalent)

QVY.2: 11 residues within 4Å: Chain A: F.58, H.62, F.126, L.133, A.136, S.137, G.138, L.322 Chain B: Y.28, Y.31 Ligands: HEM.1 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.58, A:F.58, A:L.133, A:L.133, A:L.133, A:A.136, B:Y.28, B:Y.31 Hydrogen bonds: A:A.136 QVY.4: 11 residues within 4Å: Chain A: Y.28, Y.31 Chain B: F.58, H.62, F.126, L.133, A.136, S.137, G.138, L.322 Ligands: HEM.3 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.28, A:Y.31, B:F.58, B:L.133, B:A.136 Hydrogen bonds: B:A.136 QVY.6: 11 residues within 4Å: Chain C: Y.28, Y.31 Chain D: F.58, H.62, F.126, L.133, A.136, S.137, G.138, L.322 Ligands: HEM.8 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:Y.28, C:Y.31, D:F.58, D:L.133, D:L.133, D:A.136 Hydrogen bonds: D:A.136 pi-Stacking: D:F.58 QVY.7: 11 residues within 4Å: Chain C: F.58, H.62, F.126, L.133, A.136, S.137, G.138, L.322 Chain D: Y.28, Y.31 Ligands: HEM.5 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.58, C:L.133, C:L.133, C:A.136, D:Y.28, D:Y.31 Hydrogen bonds: C:A.136 pi-Stacking: C:F.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parr, B.T. et al., Implementation of the CYP Index for the Design of Selective Tryptophan-2,3-dioxygenase Inhibitors. Acs Med.Chem.Lett. (2020)

Release Date

2020-05-06

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