7U9U

Crystal structure of human D-amino acid oxidase in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.202 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of a Novel Class of d-Amino Acid Oxidase Inhibitors Using the Schrodinger Computational Platform.

Tang, H.Jensen, K.Houang, E.McRobb, F.M.Bhat, S.Svensson, M.Bochevarov, A.Day, T.Dahlgren, M.K.Bell, J.A.Frye, L.Skene, R.J.Lewis, J.H.Osborne, J.D.Tierney, J.P.Gordon, J.A.Palomero, M.A.Gallati, C.Chapman, R.S.L.Jones, D.R.Hirst, K.L.Sephton, M.Chauhan, A.Sharpe, A.Tardia, P.Dechaux, E.A.Taylor, A.Waddell, R.D.Valentine, A.Janssens, H.B.Aziz, O.Bloomfield, D.E.Ladha, S.Fraser, I.J.Ellard, J.M.

(2022) J Med Chem 65: 6775-6802

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00118
  • Primary Citation of Related Structures:  
    7U9S, 7U9U

  • PubMed Abstract: 

    d-Serine is a coagonist of the N -methyl d-aspartate (NMDA) receptor, a key excitatory neurotransmitter receptor. In the brain, d-serine is synthesized from its l-isomer by serine racemase and is metabolized by the D-amino acid oxidase (DAO, DAAO). Many studies have linked decreased d-serine concentration and/or increased DAO expression and enzyme activity to NMDA dysfunction and schizophrenia. Thus, it is feasible to employ DAO inhibitors for the treatment of schizophrenia and other indications. Powered by the Schrödinger computational modeling platform, we initiated a research program to identify novel DAO inhibitors with the best-in-class properties. The program execution leveraged an hDAO FEP+ model to prospectively predict compound potency. A new class of DAO inhibitors with desirable properties has been discovered from this endeavor. Our modeling technology on this program has not only enhanced the efficiency of structure-activity relationship development but also helped to identify a previously unexplored subpocket for further optimization.


  • Organizational Affiliation

    Schrödinger Inc., New York, New York 10036, United States.


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: DAODAMOX
EC: 1.4.3.3
UniProt & NIH Common Fund Data Resources
Find proteins for P14920 (Homo sapiens)
Explore P14920 
Go to UniProtKB:  P14920
PHAROS:  P14920
GTEx:  ENSG00000110887 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14920
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.806α = 90
b = 73.403β = 90
c = 79.799γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
PRIME-Xrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-08
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description