SMTL ID : 3znp.1 (1 other biounit)

IN VITRO AND IN VIVO INHIBITION OF HUMAN D-AMINO ACID OXIDASE: REGULATION OF D-SERINE CONCENTRATION IN THE BRAIN

Coordinates

PDB Format Compare

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, 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, G.281, F.282, R.283, P.284, H.311, G.312, G.313, Y.314, G.315, L.316, T.317 Ligands: SE2.2 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:I.202, A:R.283 Hydrogen bonds: A:A.8, A:I.11, A:D.37, A:R.38, A:R.38, A:T.44, A:T.44, 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, A:V.184 pi-Cation interactions: A:R.38 FAD.7: 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, 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, G.281, F.282, R.283, P.284, H.311, G.312, G.313, Y.314, G.315, L.316, T.317 Ligands: SE2.8 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:I.202, B:R.283 Hydrogen bonds: B:A.8, B:I.11, B:D.37, B:R.38, 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 Water bridges: B:G.183, B:V.184, B:V.184 pi-Cation interactions: B:R.38

2 x SE2: 3-HYDROXY-2H-CHROMEN-2-ONE(Non-covalent)

SE2.2: 9 residues within 4Å: Chain A: L.51, Q.53, L.215, 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.224, A:I.230 Hydrogen bonds: A:R.283, A:R.283 Salt bridges: A:R.283 pi-Stacking: A:Y.224 SE2.8: 9 residues within 4Å: Chain B: L.51, Q.53, L.215, Y.224, Y.228, I.230, R.283, G.313 Ligands: FAD.7 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.51, B:Q.53, B:L.215, B:Y.224, B:I.230 Hydrogen bonds: B:Y.228, B:R.283, B:R.283 Salt bridges: B:R.283 pi-Stacking: B:Y.224

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: D.31, G.156, K.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.156, A:K.158 GOL.4: 2 residues within 4Å: Chain A: E.292, R.293 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.293 Water bridges: A:E.292 GOL.5: 1 residues within 4Å: Chain A: E.154 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.154 GOL.6: 5 residues within 4Å: Chain A: L.56, H.217, D.218, P.219, I.223 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.217 Water bridges: A:Y.224 GOL.9: 3 residues within 4Å: Chain B: D.31, G.156, K.158 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.31, B:D.31, B:G.156, B:K.158 GOL.10: 2 residues within 4Å: Chain B: E.292, R.293 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.293 Water bridges: B:E.292 GOL.11: 1 residues within 4Å: Chain B: E.154 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.154 GOL.12: 5 residues within 4Å: Chain B: L.56, H.217, D.218, P.219, I.223 2 PLIP interactions: 2 interactions with chain B Water bridges: B:H.217, B:Y.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hopkins, S.C. et al., Structural, Kinetic, and Pharmacodynamic Mechanisms of D-Amino Acid Oxidase Inhibition by Small Molecules. J.Med.Chem. (2013)

Release Date

2013-05-15

Peptides

D-AMINO-ACID OXIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

D-AMINO-ACID OXIDASE

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