3ZNP

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural, Kinetic, and Pharmacodynamic Mechanisms of D-Amino Acid Oxidase Inhibition by Small Molecules.

Hopkins, S.C.Heffernan, M.L.R.Saraswat, L.D.Bowen, C.A.Melnick, L.Hardy, L.W.Orsini, M.A.Allen, M.S.Koch, P.Spear, K.L.Foglesong, R.J.Soukri, M.Chytil, M.Fang, Q.K.Jones, S.W.Varney, M.A.Panatier, A.Oliet, S.H.R.Pollegioni, L.Piubelli, L.Molla, G.Nardini, M.Large, T.H.

(2013) J Med Chem 56: 3710

  • DOI: 10.1021/jm4002583
  • Primary Citation of Related Structures:  
    3ZNO, 3ZNP, 3ZNQ, 3ZNN

  • PubMed Abstract: 
  • We characterized the mechanism and pharmacodynamics of five structurally distinct inhibitors of d-amino acid oxidase. All inhibitors bound the oxidized form of human enzyme with affinity slightly higher than that of benzoate (Kd ≈ 2-4 μM). Stopped-fl ...

    We characterized the mechanism and pharmacodynamics of five structurally distinct inhibitors of d-amino acid oxidase. All inhibitors bound the oxidized form of human enzyme with affinity slightly higher than that of benzoate (Kd ≈ 2-4 μM). Stopped-flow experiments showed that pyrrole-based inhibitors possessed high affinity (Kd ≈ 100-200 nM) and slow release kinetics (k < 0.01 s(-1)) in the presence of substrate, while inhibitors with pendent aromatic groups altered conformations of the active site lid, as evidenced by X-ray crystallography, and showed slower kinetics of association. Rigid bioisosteres of benzoic acid induced a closed-lid conformation, had slower release in the presence of substrate, and were more potent than benzoate. Steady-state d-serine concentrations were described in a PK/PD model, and competition for d-serine sites on NMDA receptors was demonstrated in vivo. DAAO inhibition increased the spatiotemporal influence of glial-derived d-serine, suggesting localized effects on neuronal circuits where DAAO can exert a neuromodulatory role.


    Organizational Affiliation

    Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States. seth.hopkins@sunovion.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D-AMINO-ACID OXIDASEAB347Homo sapiensMutation(s): 0 
Gene Names: DAODAMOX
EC: 1.4.3.3
Find proteins for P14920 (Homo sapiens)
Explore P14920 
Go to UniProtKB:  P14920
NIH Common Fund Data Resources
PHAROS  P14920
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
SE2
Query on SE2

Download CCD File 
A
3-HYDROXY-2H-CHROMEN-2-ONE
C9 H6 O3
MJKVTPMWOKAVMS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SE2Ki:  13   nM  BindingDB
SE2Kd:  6300   nM  BindingDB
SE2IC50:  943   nM  BindingDB
SE2Kd:  4000   nM  BindingDB
SE2IC50:  440   nM  BindingDB
SE2Ki:  13   nM  Binding MOAD
SE2Ki:  156   nM  BindingDB
SE2Kd:  5600   nM  BindingDB
SE2IC50:  35   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.236 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.069α = 90
b = 84.069β = 90
c = 189.163γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
d*TREKdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2013-05-15
    Type: Initial release
  • Version 1.1: 2013-05-22
    Changes: Database references