SMTL ID : 8r5r.1

Structure of apo TDO with a bound inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.08 Å

Oligo State

homo-tetramer

Ligands

4 x Y5N: 3-chloranyl-~{N}-[(1~{S})-1-(6-chloranylpyridin-3-yl)-2-phenyl-ethyl]aniline

Y5N.1: 17 residues within 4Å: Chain A: F.34, H.38, F.102, L.109, P.111, A.112, G.114, F.115, Q.116, S.117, H.290, V.294, M.297, L.298 Chain B: Y.4, Y.7, L.8 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.34, A:F.102, A:L.109, A:V.294, A:M.297, A:L.298, B:Y.7 Hydrogen bonds: A:A.112, A:Q.116 pi-Stacking: A:F.34, A:H.290 Y5N.3: 17 residues within 4Å: Chain A: Y.4, Y.7, L.8 Chain B: F.34, H.38, F.102, L.109, P.111, A.112, G.114, F.115, Q.116, S.117, H.290, V.294, M.297, L.298 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.34, B:F.102, B:L.109, B:V.294, B:M.297, B:L.298, A:Y.7 Hydrogen bonds: B:A.112, B:Q.116 pi-Stacking: B:F.34, B:H.290 Y5N.5: 17 residues within 4Å: Chain C: F.34, H.38, F.102, L.109, P.111, A.112, G.114, F.115, Q.116, S.117, H.290, V.294, M.297, L.298 Chain D: Y.4, Y.7, L.8 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.34, C:F.102, C:L.109, C:V.294, C:M.297, C:L.298, D:Y.7 Hydrogen bonds: C:A.112, C:Q.116 pi-Stacking: C:F.34, C:H.290 Y5N.7: 17 residues within 4Å: Chain C: Y.4, Y.7, L.8 Chain D: F.34, H.38, F.102, L.109, P.111, A.112, G.114, F.115, Q.116, S.117, H.290, V.294, M.297, L.298 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.34, D:F.102, D:L.109, D:V.294, D:M.297, D:L.298, C:Y.7 Hydrogen bonds: D:A.112, D:Q.116 pi-Stacking: D:F.34, D:H.290

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

ZIQ.2: 11 residues within 4Å: Chain A: V.64, R.65, E.67, W.170, R.173, T.174, P.175, I.257, R.265, F.266, P.269 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.170, A:T.174, A:I.257, A:F.266, A:F.266, A:P.269 Hydrogen bonds: A:E.67, A:W.170 Salt bridges: A:R.65, A:R.173 ZIQ.4: 11 residues within 4Å: Chain B: V.64, R.65, E.67, W.170, R.173, T.174, P.175, I.257, R.265, F.266, P.269 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:W.170, B:P.175, B:I.257, B:F.266, B:F.266, B:P.269 Hydrogen bonds: B:E.67, B:E.67, B:W.170 Salt bridges: B:R.65, B:R.173 ZIQ.6: 11 residues within 4Å: Chain C: V.64, R.65, E.67, W.170, R.173, T.174, P.175, I.257, R.265, F.266, P.269 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:W.170, C:P.175, C:I.257, C:F.266, C:F.266, C:P.269 Hydrogen bonds: C:V.64, C:E.67, C:E.67, C:W.170 Salt bridges: C:R.65, C:R.173 ZIQ.8: 11 residues within 4Å: Chain D: V.64, R.65, E.67, W.170, R.173, T.174, P.175, I.257, R.265, F.266, P.269 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:W.170, D:T.174, D:I.257, D:F.266, D:F.266, D:P.269 Hydrogen bonds: D:E.67, D:W.170 Salt bridges: D:R.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lotz-Jenne, C. et al., Discovery and binding mode of a small molecule inhibitor of the apo form of human TDO2. Biorxiv (2024)

Release Date

2024-01-17

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

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