SMTL ID : 3w4k.3 (2 other biounits)

Crystal Structure of human DAAO in complex with coumpound 13

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.86 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 37 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, V.47, 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: 3LD.2 25 PLIP interactions: 25 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:T.44, 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:Y.314, A:G.315, A:L.316, A:T.317, A:T.317 pi-Cation interactions: A:R.38 FAD.3: 34 residues within 4Å: Chain B: 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, Y.228, R.283, H.311, G.312, G.313, Y.314, G.315, L.316, T.317 Ligands: 3LD.4 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:R.283 Hydrogen bonds: B:A.8, 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: 37 residues within 4Å: Chain C: I.6, G.7, A.8, G.9, V.10, I.11, G.12, 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, I.202, Y.228, G.281, F.282, R.283, G.312, G.313, Y.314, G.315, L.316, T.317 Ligands: 3LD.6 27 PLIP interactions: 27 interactions with chain C Hydrophobic interactions: C:I.202, C:R.283 Hydrogen bonds: C:A.8, C:G.9, C:V.10, C:I.11, C:G.12, C:D.37, C:R.38, C:R.38, C:R.38, C:R.38, C:T.43, 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: 38 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, V.47, 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, H.311, G.312, G.313, Y.314, G.315, L.316, T.317 Ligands: 3LD.8 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:V.47, D:I.202, D:R.283 Hydrogen bonds: D:A.8, D:V.10, D:I.11, D:D.37, D:D.37, D:R.38, 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:G.315, D:L.316, D:T.317, D:T.317

4 x 3LD: 3-hydroxy-6-(2-phenylethyl)pyridazin-4(1H)-one(Non-covalent)(Covalent)

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

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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