1D3H

HUMAN DIHYDROOROTATE DEHYDROGENASE COMPLEXED WITH ANTIPROLIFERATIVE AGENT A771726

Structural Biology Knowledgebase: 1D3H SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.185
  • R-Value Work: 0.162

Literature

Macromolecules
Sequence Display for 1D3H

Classification: OXIDOREDUCTASE

Total Structure Weight: 40894.70

Macromolecule Entities
Molecule Chains Length Organism Details
DIHYDROOROTATE DEHYDROGENASE A 367 Homo sapiens EC#: 1.3.5.2 IUBMB
Gene Name(s): DHODH Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: inferred by homology | Group: MONOTOPIC MEMBRANE PROTEINS

Subgroup Name: Dihydroorotate Dehydrogenases (DHODH, class 2)

Protein Name: Dihydroorotate Dehydrogenase, apo form


Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
FMN
Query on FMN

A FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE (Synonym)
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
A26
Query on A26

A (2Z)-2-cyano-3-hydroxy-N-[4-(trifluoromethyl)phenyl]but- 2-enamide
ANTIPROLIFERATIVE AGENT A771726 (Synonym)
C12 H9 F3 N2 O2
UTNUDOFZCWSZMS-YFHOEESVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ORO
Query on ORO

A OROTIC ACID
C5 H4 N2 O4
PXQPEWDEAKTCGB-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
A26 IC50: 9 - 5012 nM (88 - 100) BindingDB
Ki: 30 - 2700 nM (100) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.185
  • R-Value Work: 0.162
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 90.61 α = 90.00
b = 90.61 β = 90.00
c = 122.41 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-09-29
  • Released Date: 2000-08-13
  • Deposition author(s): Liu, S., Neidhardt, E.A., Grossman, T.H., Ocain, T., Clardy, J.

Revision History

  • 2012-07-18
    Type: Non-polymer description | Details: --
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4