SMTL ID : 3znn.1

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 1.90 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, 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: 4WL.2, GOL.5 29 PLIP interactions: 29 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: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.12, A:T.44, A:G.183, A:G.183, A:V.184 FAD.10: 38 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, 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: 4WL.11 32 PLIP interactions: 32 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.43, B:T.44, B:T.44, 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.12, B:D.37, B:K.163, B:K.163, B:G.183, B:G.183, B:V.184

2 x 4WL: 4H-THIENO[3,2-B]PYROLE-5-CARBOXYLIC ACID(Non-covalent)

4WL.2: 9 residues within 4Å: Chain A: L.51, Q.53, Y.224, Y.228, I.230, R.283, G.313 Ligands: FAD.1, GOL.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.224, A:Y.228 Hydrogen bonds: A:Y.228, A:Y.228, A:G.313 Salt bridges: A:R.283 4WL.11: 9 residues within 4Å: Chain B: L.51, Q.53, L.215, Y.224, Y.228, I.230, R.283, G.313 Ligands: FAD.10 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.224, B:Y.228 Hydrogen bonds: B:Y.228, B:G.313 Water bridges: B:Y.224 Salt bridges: B:R.283

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: K.158, F.159, F.160 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.159 GOL.4: 6 residues within 4Å: Chain A: F.98, H.99, E.100, I.102, H.217, P.219 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.99, A:E.100, A:H.217 Water bridges: A:D.218 GOL.5: 6 residues within 4Å: Chain A: D.37, R.38, K.163, W.185 Ligands: FAD.1, GOL.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.37 GOL.6: 8 residues within 4Å: Chain A: T.45, D.46, A.48, A.49, E.140, G.141, K.142, K.204 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.45, A:G.141, A:K.142, A:K.204 Water bridges: A:A.49, A:E.140, A:K.204, A:T.237 GOL.7: 8 residues within 4Å: Chain A: Q.53, P.54, L.56, L.215, H.217, I.223, Y.224 Ligands: 4WL.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.53, A:L.56 GOL.8: 6 residues within 4Å: Chain A: R.38, W.185, W.247, E.249, F.282 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.38, A:W.247 GOL.9: 2 residues within 4Å: Chain A: E.294, Q.295 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.295 Water bridges: A:E.292, A:R.293, A:R.293, A:Q.295 GOL.12: 5 residues within 4Å: Chain B: P.193, L.194, Q.196, V.285, P.287 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.193, B:V.285 GOL.13: 4 residues within 4Å: Chain B: G.187, R.191, D.192, P.193 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.192 GOL.14: 4 residues within 4Å: Chain B: H.99, D.127, Y.128, G.129 No protein-ligand interaction detected (PLIP) GOL.15: 4 residues within 4Å: Chain A: H.80 Chain B: D.123, M.124, P.126 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:M.124, A:H.80

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
B

D-AMINO-ACID OXIDASE

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