SMTL ID : 7u9u.2 (1 other biounit)

Crystal structure of human D-amino acid oxidase in complex with inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 48 residues within 4Å: Chain A: I.6, G.7, A.8, G.9, V.10, I.11, G.12, Y.35, A.36, D.37, R.38, F.39, T.43, T.44, T.45, V.47, A.48, A.49, G.50, L.51, W.52, Q.53, R.162, K.163, V.164, C.181, T.182, G.183, W.185, A.188, L.189, G.198, G.200, Q.201, I.202, Y.228, G.281, F.282, R.283, P.284, H.311, G.312, G.313, Y.314, G.315, L.316, T.317 Ligands: M89.2 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:V.47, A:I.202, A:R.283 Hydrogen bonds: A:A.8, A:G.9, A:I.11, A:D.37, A:R.38, A:R.38, A:T.44, A:T.44, A:T.45, A:T.45, A:T.45, A:A.49, A:G.50, A:L.51, A:L.51, A:V.164, A:V.164, A:G.312, A:Y.314, A:G.315, A:L.316, A:T.317, A:T.317 Water bridges: A:G.12, A:D.37, A:G.183, A:V.184, A:H.311 FAD.3: 48 residues within 4Å: Chain B: I.6, G.7, A.8, G.9, V.10, I.11, G.12, Y.35, A.36, D.37, R.38, F.39, T.43, T.44, T.45, V.47, A.48, A.49, G.50, L.51, W.52, Q.53, R.162, K.163, V.164, C.181, T.182, G.183, W.185, A.188, L.189, G.198, G.200, Q.201, I.202, Y.228, G.281, F.282, R.283, P.284, H.311, G.312, G.313, Y.314, G.315, L.316, T.317 Ligands: M89.4 31 PLIP interactions: 31 interactions with chain B Hydrophobic interactions: B:V.47, B:I.202, B:R.283 Hydrogen bonds: B:A.8, B:G.9, B:I.11, B:D.37, B:R.38, B:R.38, B:T.44, B:T.44, B:T.45, B:T.45, B:T.45, B:A.49, B:G.50, B:L.51, B:L.51, B:V.164, B:V.164, B:G.312, B:Y.314, B:G.315, B:L.316, B:T.317, B:T.317 Water bridges: B:G.12, B:D.37, B:G.183, B:V.184, B:H.311

2 x M89: (3R)-3-(5,6-dioxo-1,4,5,6-tetrahydropyrazin-2-yl)-2,3-dihydro-1,4-benzoxathiine-7-carbonitrile(Non-covalent)

M89.2: 16 residues within 4Å: Chain A: A.49, L.51, Q.53, P.54, Y.55, L.56, L.215, H.217, I.223, Y.224, Y.228, I.230, R.283, G.313, Y.314 Ligands: FAD.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.224, A:Y.224 Hydrogen bonds: A:L.56, A:Y.228, A:Y.228, A:R.283, A:R.283, A:G.313 Water bridges: A:Y.224, A:Y.224 pi-Stacking: A:Y.224 M89.4: 16 residues within 4Å: Chain B: A.49, L.51, Q.53, P.54, Y.55, L.56, L.215, H.217, I.223, Y.224, Y.228, I.230, R.283, G.313, Y.314 Ligands: FAD.3 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.224, B:Y.224 Hydrogen bonds: B:L.56, B:Y.228, B:Y.228, B:R.283, B:R.283, B:G.313 Water bridges: B:Y.224, B:Y.224 pi-Stacking: B:Y.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tang, H. et al., Discovery of a Novel Class of d-Amino Acid Oxidase Inhibitors Using the Schrodinger Computational Platform. J.Med.Chem. (2022)

Release Date

2022-06-08

Peptides

D-amino-acid oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

D-amino-acid oxidase

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