4QFD

Co-crystal structure of compound 2 (3-(7-hydroxy-2-oxo-4-phenyl-2H-chromen-6-yl)propanoic acid) and FAD bound to human DAAO at 2.85A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.9 of the entry. See complete history


Literature

Novel human D-amino acid oxidase inhibitors stabilize an active-site lid-open conformation.

Terry-Lorenzo, R.T.Chun, L.E.Brown, S.P.Heffernan, M.L.Fang, Q.K.Orsini, M.A.Pollegioni, L.Hardy, L.W.Spear, K.L.Large, T.H.

(2014) Biosci Rep 34

  • DOI: https://doi.org/10.1042/BSR20140071
  • Primary Citation of Related Structures:  
    4QFC, 4QFD

  • PubMed Abstract: 

    The NMDAR (N-methyl-D-aspartate receptor) is a central regulator of synaptic plasticity and learning and memory. hDAAO (human D-amino acid oxidase) indirectly reduces NMDAR activity by degrading the NMDAR co-agonist D-serine. Since NMDAR hypofunction is thought to be a foundational defect in schizophrenia, hDAAO inhibitors have potential as treatments for schizophrenia and other nervous system disorders. Here, we sought to identify novel chemicals that inhibit hDAAO activity. We used computational tools to design a focused, purchasable library of compounds. After screening this library for hDAAO inhibition, we identified the structurally novel compound, 'compound 2' [3-(7-hydroxy-2-oxo-4-phenyl-2H-chromen-6-yl)propanoic acid], which displayed low nM hDAAO inhibitory potency (Ki=7 nM). Although the library was expected to enrich for compounds that were competitive for both D-serine and FAD, compound 2 actually was FAD uncompetitive, much like canonical hDAAO inhibitors such as benzoic acid. Compound 2 and an analog were independently co-crystalized with hDAAO. These compounds stabilized a novel conformation of hDAAO in which the active-site lid was in an open position. These results confirm previous hypotheses regarding active-site lid flexibility of mammalian D-amino acid oxidases and could assist in the design of the next generation of hDAAO inhibitors.


  • Organizational Affiliation

    *Discovery Research Department, Sunovion Pharmaceuticals, Marlborough, MA 01752, U.S.A.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-amino-acid oxidase
A, B
347Homo sapiensMutation(s): 0 
Gene Names: DAMOXDAODAO DAMOX
EC: 1.4.3.3
UniProt & NIH Common Fund Data Resources
Find proteins for P14920 (Homo sapiens)
Go to UniProtKB:  P14920
PHAROS:  P14920
GTEx:  ENSG00000110887 
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.49α = 90
b = 86.49β = 90
c = 187.97γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2014-10-15
    Changes: Structure summary
  • Version 1.2: 2014-11-26
    Changes: Database references
  • Version 1.3: 2014-12-31
    Changes: Database references
  • Version 1.4: 2015-03-04
    Changes: Database references
  • Version 1.5: 2015-03-18
    Changes: Database references
  • Version 1.6: 2015-03-25
    Changes: Database references
  • Version 1.7: 2015-06-17
    Changes: Database references
  • Version 1.8: 2015-07-15
    Changes: Database references
  • Version 1.9: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description