2WV8

Complex of human dihydroorotate dehydrogenase with the inhibitor 221290


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inhibition of Human Dhodh by 4-Hydroxycoumarins, Fenamic Acids, and N-(Alkylcarbonyl)Anthranilic Acids Identified by Structure-Guided Fragment Selection.

Fritzson, I.Svensson, B.Al-Karadaghi, S.Walse, B.Wellmar, U.Nilsson, U.J.Da Graca Thrige, D.Jonsson, S.

(2010) Chemmedchem 5: 608

  • DOI: 10.1002/cmdc.200900454

  • PubMed Abstract: 
  • A strategy that combines virtual screening and structure-guided selection of fragments was used to identify three unexplored classes of human DHODH inhibitor compounds: 4-hydroxycoumarins, fenamic acids, and N-(alkylcarbonyl)anthranilic acids. Struct ...

    A strategy that combines virtual screening and structure-guided selection of fragments was used to identify three unexplored classes of human DHODH inhibitor compounds: 4-hydroxycoumarins, fenamic acids, and N-(alkylcarbonyl)anthranilic acids. Structure-guided selection of fragments targeting the inner subsite of the DHODH ubiquinone binding site made these findings possible with screening of fewer than 300 fragments in a DHODH assay. Fragments from the three inhibitor classes identified were subsequently chemically expanded to target an additional subsite of hydrophobic character. All three classes were found to exhibit distinct structure-activity relationships upon expansion. The novel N-(alkylcarbonyl)anthranilic acid class shows the most promising potency against human DHODH, with IC(50) values in the low nanomolar range. The structure of human DHODH in complex with an inhibitor of this class is presented.


    Organizational Affiliation

    Active Biotech Research AB, Box 724, 220 07 Lund, Sweden. ingela.fritzson@activebiotech.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIHYDROOROTATE DEHYDROGENASE, MITOCHONDRIAL
A
365Homo 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 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
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
ACT
Query on ACT

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Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
DDQ
Query on DDQ

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Download CCD File 
A
DECYLAMINE-N,N-DIMETHYL-N-OXIDE
C12 H27 N O
ZRKZFNZPJKEWPC-UHFFFAOYSA-N
 Ligand Interaction
ORO
Query on ORO

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Download CCD File 
A
OROTIC ACID
C5 H4 N2 O4
PXQPEWDEAKTCGB-UHFFFAOYSA-N
 Ligand Interaction
VGN
Query on VGN

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Download CCD File 
A
2-ACETAMIDO-5-(4-PHENYLPHENYL)BENZOIC ACID
C21 H17 N O3
XXPKIBVYLUEVCV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VGNIC50: 210 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.185 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 90.660α = 90.00
b = 90.660β = 90.00
c = 122.840γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-25
    Type: Initial release
  • Version 1.1: 2012-04-25
    Type: Database references, Version format compliance
  • Version 1.2: 2018-01-17
    Type: Data collection