1D3H

HUMAN DIHYDROOROTATE DEHYDROGENASE COMPLEXED WITH ANTIPROLIFERATIVE AGENT A771726

• PDB DOI:  https://doi.org/10.2210/pdb1D3H/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.185 
• R-Value Work: 0.162 
• R-Value Observed: 0.162 

Literature

Structures of human dihydroorotate dehydrogenase in complex with antiproliferative agents.

Liu, S., Neidhardt, E.A., Grossman, T.H., Ocain, T., Clardy, J.

(2000) Structure 8: 25-33

• PubMed: 10673429 
• DOI: https://doi.org/10.1016/s0969-2126(00)00077-0
• Primary Citation of Related Structures:  
  1D3G, 1D3H


• PubMed Abstract: 
  

  Dihydroorotate dehydrogenase (DHODH) catalyzes the fourth committed step in the de novo biosynthesis of pyrimidines. As rapidly proliferating human T cells have an exceptional requirement for de novo pyrimidine biosynthesis, small molecule DHODH inhibitors constitute an attractive therapeutic approach to autoimmune diseases, immunosuppression, and cancer. Neither the structure of human DHODH nor any member of its family was known.

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Organizational Affiliation: 

Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.89 kDa 
• Atom Count: 3,158 
• Modelled Residue Count: 364 
• Deposited Residue Count: 367 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIHYDROOROTATE DEHYDROGENASE	A	367	Homo sapiens	Mutation(s): 0  Gene Names: DHODH EC: 1.3.3.1 (PDB Primary Data), 1.3.5.2 (UniProt) Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q02127 (Homo sapiens) Explore Q02127  Go to UniProtKB:  Q02127
PHAROS:  Q02127

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	E [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
A26	D [auth A]	(2Z)-2-cyano-3-hydroxy-N-[4-(trifluoromethyl)phenyl]but-2-enamide C12 H9 F3 N2 O2 UTNUDOFZCWSZMS-YFHOEESVSA-N
ORO	F [auth A]	OROTIC ACID C5 H4 N2 O4 PXQPEWDEAKTCGB-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
A26	BindingDB:  1D3H	IC50: min: 17, max: 5012 (nM) from 15 assay(s)
		EC50: min: 8900, max: 8913 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.185 
• R-Value Work: 0.162 
• R-Value Observed: 0.162 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.61	α = 90
b = 90.61	β = 90
c = 122.41	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHELXS	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2000-08-13
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2012-07-18
  Changes: Non-polymer description