SMTL ID : 4qfc.1

Co-crystal structure of compound 3 (4-hydroxy-6-[2-(7-hydroxy-2-oxo-4-phenyl-2h-chromen-6-yl)ethyl]pyridazin-3(2h)-one) and FAD bound to human DAAO at 2.4A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 38 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, H.311, G.312, G.313, Y.314, G.315, L.316, T.317 Ligands: 31T.2 28 PLIP interactions: 28 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:G.12, A:D.37, A:D.37, A:R.38, A:T.43, 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:G.315, A:L.316, A:T.317, A:T.317 Water bridges: A:G.183, A:V.184 FAD.4: 38 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, 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, H.311, G.312, G.313, Y.314, G.315, L.316, T.317 Ligands: 31T.5 29 PLIP interactions: 29 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:T.43, B:T.43, 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.183, B:G.312, B:Y.314, B:G.315, B:L.316, B:T.317, B:T.317 Water bridges: B:G.12, B:V.184, B:V.184

2 x 31T: 4-hydroxy-6-[2-(7-hydroxy-2-oxo-4-phenyl-2H-chromen-6-yl)ethyl]pyridazin-3(2H)-one(Non-covalent)

31T.2: 14 residues within 4Å: Chain A: L.51, Q.53, P.54, Y.55, L.56, L.215, Y.224, S.226, Y.228, I.230, G.240, R.283, G.313 Ligands: FAD.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.215, A:Y.224, A:Y.224, A:Y.228, A:I.230 Hydrogen bonds: A:L.51, A:L.56, A:Y.228, A:Y.228, A:R.283, A:G.313 Water bridges: A:S.57 Salt bridges: A:H.217 pi-Stacking: A:Y.55, A:Y.228 pi-Cation interactions: A:H.217 31T.5: 13 residues within 4Å: Chain B: L.51, Q.53, P.54, Y.55, L.56, L.215, Y.224, S.226, Y.228, I.230, R.283, G.313 Ligands: FAD.4 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Q.53, B:L.215, B:Y.224, B:Y.224, B:Y.228, B:I.230 Hydrogen bonds: B:Y.55, B:L.56, B:Y.228, B:R.283, B:G.313 Salt bridges: B:H.217 pi-Stacking: B:Y.55, B:Y.55, B:Y.228 pi-Cation interactions: B:H.217

1 x K: POTASSIUM ION(Non-covalent)

K.3: 3 residues within 4Å: Chain B: L.122, F.125, Y.128 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:L.122, B:F.125, B:Y.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Terry-Lorenzo, R.T. et al., Novel human D-amino acid oxidase inhibitors stabilize an active-site lid-open conformation. Biosci.Rep. (2014)

Release Date

2014-07-16

Peptides

D-amino-acid oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D-amino-acid oxidase

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