3KVJ

Crystal Structure of Human Dihydroorotate Dehydrogenase (DHODH) with Amino-Benzoic Acid Inhibitor 105 at 1.94A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

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Ligand Structure Quality Assessment 


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:  
    3KVJ, 3KVK, 3KVL, 3KVM

  • 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 found to be structurally different from the corresponding compounds initially identified by virtual screening ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dihydroorotate dehydrogenase, mitochondrialA390Homo sapiensMutation(s): 0 
Gene Names: DHODH
EC: 1.3.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q02127 (Homo sapiens)
Explore Q02127 
Go to UniProtKB:  Q02127
PHAROS:  Q02127
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
C [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
1X5 (Subject of Investigation/LOI)
Query on 1X5

Download Ideal Coordinates CCD File 
G [auth A]2-[(cyclopropylcarbonyl)amino]-5-[methyl(pyridin-3-ylmethyl)amino]benzoic acid
C18 H19 N3 O3
XLLCMCCHDIWDPC-UHFFFAOYSA-N
 Ligand Interaction
DET (Subject of Investigation/LOI)
Query on DET

Download Ideal Coordinates CCD File 
E [auth A]UNDECYLAMINE-N,N-DIMETHYL-N-OXIDE
C13 H29 N O
OZHBUVQCJMARBN-UHFFFAOYSA-N
 Ligand Interaction
DOR (Subject of Investigation/LOI)
Query on DOR

Download Ideal Coordinates CCD File 
D [auth A](4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID
C5 H6 N2 O4
UFIVEPVSAGBUSI-REOHCLBHSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
F [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
1X5 BindingDB:  3KVJ IC50: 100 (nM) from 1 assay(s)
Binding MOAD:  3KVJ IC50: 100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.838α = 90
b = 90.838β = 90
c = 123.1γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACTdata extraction
CNXrefinement

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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