SMTL ID : 9ezj.1

Apo human TDO in complex with a bound inhibitor (Cpd-4)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

homo-tetramer

Ligands

4 x ZIQ: alpha-methyl-L-tryptophan(Non-covalent)

ZIQ.1: 11 residues within 4Å: Chain A: V.99, R.100, E.102, W.205, R.208, T.209, P.210, I.292, R.300, F.301, P.304 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.205, A:P.210, A:I.292, A:F.301, A:P.304 Hydrogen bonds: A:E.102, A:W.205 Salt bridges: A:R.100, A:R.208 pi-Stacking: A:W.205 ZIQ.3: 11 residues within 4Å: Chain B: V.99, R.100, E.102, W.205, R.208, T.209, P.210, I.292, R.300, F.301, P.304 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:W.205, B:P.210, B:I.292, B:F.301, B:P.304 Hydrogen bonds: B:E.102, B:E.102, B:W.205 Salt bridges: B:R.100, B:R.208 pi-Stacking: B:W.205 ZIQ.5: 11 residues within 4Å: Chain C: V.99, R.100, E.102, W.205, R.208, T.209, P.210, I.292, R.300, F.301, P.304 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:W.205, C:P.210, C:I.292, C:F.301, C:P.304 Hydrogen bonds: C:E.102, C:E.102, C:W.205 Salt bridges: C:R.100, C:R.208 pi-Stacking: C:W.205 ZIQ.7: 11 residues within 4Å: Chain D: V.99, R.100, E.102, W.205, R.208, T.209, P.210, I.292, R.300, F.301, P.304 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:W.205, D:P.210, D:I.292, D:F.301, D:P.304 Hydrogen bonds: D:E.102, D:W.205 Salt bridges: D:R.100, D:R.208 pi-Stacking: D:W.205

4 x 01: ethyl (9~{R})-2-methoxy-4-oxidanylidene-9-[[(1~{S})-1-phenylethyl]-[(2-propan-2-ylphenyl)carbamoyl]amino]-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidine-3-carboxylate

01.2: 17 residues within 4Å: Chain A: F.69, H.73, Y.76, F.80, F.126, L.129, F.137, A.147, F.150, Q.151, S.152, F.155, W.321, H.325, V.329, L.333 Chain D: Y.39 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.76, A:F.80, A:F.126, A:L.129, A:F.137, A:A.147, A:F.150, A:F.155, A:W.321, A:V.329, A:L.333 Hydrogen bonds: A:H.73, A:S.152 Salt bridges: A:H.325 pi-Stacking: A:F.69, A:H.325 01.4: 18 residues within 4Å: Chain B: F.69, H.73, Y.76, E.77, F.80, F.126, L.129, F.137, A.147, F.150, Q.151, S.152, F.155, W.321, H.325, V.329, L.333 Chain C: Y.39 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.76, B:F.80, B:F.126, B:L.129, B:F.137, B:A.147, B:F.150, B:W.321, B:W.321, B:V.329, B:L.333 Hydrogen bonds: B:H.73, B:S.152 Salt bridges: B:H.325 pi-Stacking: B:F.69, B:H.325 01.6: 17 residues within 4Å: Chain B: Y.39 Chain C: F.69, H.73, Y.76, E.77, F.80, F.126, L.129, F.137, F.150, Q.151, S.152, F.155, W.321, H.325, V.329, L.333 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:Y.76, C:F.80, C:F.126, C:L.129, C:F.137, C:F.150, C:F.150, C:F.155, C:W.321, C:V.329, C:L.333, C:L.333 Hydrogen bonds: C:H.73, C:S.152 Salt bridges: C:H.325 pi-Stacking: C:F.69, C:H.325 01.8: 17 residues within 4Å: Chain A: Y.39 Chain D: F.69, H.73, Y.76, E.77, F.80, F.126, L.129, F.137, F.150, Q.151, S.152, F.155, W.321, H.325, V.329, L.333 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:Y.76, D:F.80, D:F.126, D:L.129, D:F.137, D:F.150, D:F.150, D:F.155, D:W.321, D:V.329, D:L.333, D:L.333 Hydrogen bonds: D:H.73, D:S.152 Salt bridges: D:H.325 pi-Stacking: D:F.69, D:H.325

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lotz-Jenne, C. et al., Discovery and binding mode of small molecule inhibitors of the apo form of human TDO2. Sci Rep (2024)

Release Date

2024-06-05

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