3KVK

Crystal structure of human dihydroorotate dehydrogenase (DHODH) with amino-benzoic acid inhibitor 641 at 2.05A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of novel inhibitors for DHODH via virtual screening and X-ray crystallographic structures.

McLean, L.R.Zhang, Y.Degnen, W.Peppard, J.Cabel, D.Zou, C.Tsay, J.T.Subramaniam, A.Vaz, R.J.Li, Y.

(2010) Bioorg.Med.Chem.Lett. 20: 1981-1984

  • DOI: 10.1016/j.bmcl.2010.01.115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Amino-benzoic acid derivatives 1-4 were found to be inhibitors for DHODH by virtual screening, biochemical, and X-ray crystallographic studies. X-ray structures showed that 1 and 2 bind to DHODH as predicted by virtual screening, but 3 and 4 were fou ...

    Amino-benzoic acid derivatives 1-4 were found to be inhibitors for DHODH by virtual screening, biochemical, and X-ray crystallographic studies. X-ray structures showed that 1 and 2 bind to DHODH as predicted by virtual screening, but 3 and 4 were found to be structurally different from the corresponding compounds initially identified by virtual screening.


    Organizational Affiliation

    Discovery Research, Sanofi-aventis, Bridgewater, NJ 08807, USA. Larry.Mclean@sanofi-aventis.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydroorotate dehydrogenase, mitochondrial
A
390Homo sapiensMutation(s): 0 
Gene Names: DHODH
EC: 1.3.5.2
Find proteins for Q02127 (Homo sapiens)
Go to Gene View: DHODH
Go to UniProtKB:  Q02127
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DET
Query on DET

Download SDF File 
Download CCD File 
A
UNDECYLAMINE-N,N-DIMETHYL-N-OXIDE
C13 H29 N O
OZHBUVQCJMARBN-UHFFFAOYSA-N
 Ligand Interaction
6X1
Query on 6X1

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Download CCD File 
A
2-{[(3,5-dichlorophenyl)carbamoyl]amino}benzoic acid
C14 H10 Cl2 N2 O3
PIWYMPXOKMFVER-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FMN
Query on FMN

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Download CCD File 
A
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
DOR
Query on DOR

Download SDF File 
Download CCD File 
A
(4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID
DIHYDROOROTIC ACID
C5 H6 N2 O4
UFIVEPVSAGBUSI-REOHCLBHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6X1IC50: 700 nM (100) BINDINGDB
6X1IC50: 700 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.185 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 90.908α = 90.00
b = 90.908β = 90.00
c = 123.077γ = 120.00
Software Package:
Software NamePurpose
CNXrefinement
CNSrefinement
DENZOdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-11-30 
  • Released Date: 2010-03-02 
  • Deposition Author(s): McLean, L., Zhang, Y.

Revision History 

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description