SMTL ID : 3w4j.3 (2 other biounits)

Crystal Structure of human DAAO in complex with coumpound 12

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.74 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 36 residues within 4Å: Chain A: I.6, G.7, A.8, G.9, V.10, I.11, A.36, D.37, R.38, T.43, T.44, T.45, A.48, A.49, G.50, L.51, R.162, K.163, V.164, C.181, T.182, G.183, W.185, L.189, I.202, Y.228, G.281, R.283, P.284, G.312, G.313, Y.314, G.315, L.316, T.317 Ligands: 2LD.2 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:I.202 Hydrogen bonds: A:A.8, A:G.9, A:V.10, A:I.11, A:D.37, A:R.38, A:R.38, A:R.38, A:T.44, 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:G.315, A:L.316, A:T.317, A:T.317 pi-Cation interactions: A:R.38 FAD.3: 36 residues within 4Å: Chain B: I.6, G.7, A.8, G.9, V.10, I.11, Y.35, A.36, D.37, R.38, T.43, T.44, T.45, A.48, A.49, G.50, L.51, R.162, K.163, V.164, C.181, T.182, G.183, W.185, L.189, I.202, Y.228, G.281, R.283, G.312, G.313, Y.314, G.315, L.316, T.317 Ligands: 2LD.4 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:T.44, B:I.202, B:R.283 Hydrogen bonds: B:A.8, B:V.10, B:I.11, B:D.37, B:R.38, B:T.44, 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:G.315, B:L.316, B:T.317 FAD.5: 35 residues within 4Å: Chain C: I.6, G.7, A.8, G.9, V.10, I.11, A.36, D.37, R.38, T.43, T.44, T.45, A.48, A.49, G.50, L.51, R.162, K.163, V.164, C.181, T.182, G.183, W.185, I.202, Y.228, G.281, R.283, H.311, G.312, G.313, Y.314, G.315, L.316, T.317 Ligands: 2LD.6 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:I.202, C:R.283 Hydrogen bonds: C:A.8, C:G.9, C:I.11, C:G.12, C:D.37, C:R.38, C:R.38, C:T.44, C:T.44, C:T.45, C:T.45, C:A.49, C:G.50, C:L.51, C:L.51, C:V.164, C:V.164, C:G.312, C:G.315, C:L.316, C:T.317 pi-Cation interactions: C:R.38 FAD.7: 35 residues within 4Å: Chain D: I.6, G.7, A.8, G.9, V.10, I.11, A.36, D.37, R.38, T.43, T.44, T.45, A.48, A.49, G.50, L.51, R.162, K.163, V.164, C.181, T.182, G.183, W.185, L.189, I.202, Y.228, R.283, H.311, G.312, G.313, Y.314, G.315, L.316, T.317 Ligands: 2LD.8 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:I.202, D:R.283 Hydrogen bonds: D:A.8, D:G.9, D:I.11, D:D.37, D:D.37, D:D.37, D:R.38, D:T.44, D:T.44, D:T.45, D:T.45, D:A.49, D:G.50, D:L.51, D:L.51, D:V.164, D:V.164, D:G.312, D:Y.314, D:G.315, D:L.316, D:T.317, D:T.317

4 x 2LD: 3-hydroxy-5-(2-phenylethyl)pyridin-2(1H)-one(Non-covalent)

2LD.2: 10 residues within 4Å: Chain A: L.51, Q.53, L.215, H.217, Y.224, Y.228, I.230, R.283, G.313 Ligands: FAD.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.51, A:Q.53, A:L.215, A:Y.228, A:I.230 Hydrogen bonds: A:Y.228, A:R.283, A:G.313 pi-Stacking: A:Y.224 2LD.4: 10 residues within 4Å: Chain B: L.51, Q.53, L.215, H.217, Y.224, Y.228, I.230, R.283, G.313 Ligands: FAD.3 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.51, B:Q.53, B:Q.53, B:L.215, B:Y.228, B:I.230 Hydrogen bonds: B:Y.228, B:Y.228, B:R.283, B:G.313 pi-Stacking: B:Y.224, B:Y.224 2LD.6: 9 residues within 4Å: Chain C: Q.53, L.215, H.217, Y.224, Y.228, I.230, R.283, G.313 Ligands: FAD.5 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:Q.53, C:L.215, C:Y.224, C:Y.228, C:I.230 Hydrogen bonds: C:Y.228, C:R.283, C:G.313 2LD.8: 10 residues within 4Å: Chain D: Q.53, L.215, H.217, I.223, Y.224, Y.228, I.230, R.283, G.313 Ligands: FAD.7 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:Q.53, D:L.215, D:I.223, D:Y.228, D:I.230 Hydrogen bonds: D:Y.228, D:R.283, D:G.313

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hondo, T. et al., 4-Hydroxypyridazin-3(2H)-one Derivatives as Novel d-Amino Acid Oxidase Inhibitors. J.Med.Chem. (2013)

Release Date

2013-05-29

Peptides

D-amino-acid oxidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

D-amino-acid oxidase

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