5K9D | pdb_00005k9d

Crystal structure of human dihydroorotate dehydrogenase at 1.7 A resolution

• PDB DOI: https://doi.org/10.2210/pdb5K9D/pdb

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


• Deposited: 2016-05-31 Released: 2016-10-12 
• Deposition Author(s): Lewis, T.A., Sykes, D.B., Law, J.M., Munoz, B., Scadden, D.T., Rustiguel, J.K., Nonato, M.C., Schreiber, S.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.160 (Depositor), 0.163 (DCC) 
• R-Value Work: 
  0.136 (Depositor), 0.139 (DCC) 
• R-Value Observed: 
  0.138 (Depositor) 

Starting Model: experimental

Literature

Development of ML390: A Human DHODH Inhibitor That Induces Differentiation in Acute Myeloid Leukemia.

Lewis, T.A., Sykes, D.B., Law, J.M., Munoz, B., Rustiguel, J.K., Nonato, M.C., Scadden, D.T., Schreiber, S.L.

(2016) ACS Med Chem Lett 7: 1112-1117

• PubMed: 27994748 
• DOI: https://doi.org/10.1021/acsmedchemlett.6b00316
• Primary Citation Related Structures: 
  5K9C, 5K9D


• PubMed Abstract: 
  

  Homeobox transcription factor A9 (HoxA9) is overexpressed in 70% of patients diagnosed with acute myeloid leukemia (AML), whereas only a small subset of AML patients respond to current differentiation therapies. A cell line overexpressing HoxA9 was derived from the bone marrow of a lysozyme-GFP mouse. In this fashion, GFP served as an endogenous reporter of differentiation, permitting a high-throughput phenotypic screen against the MLPCN library. Two chemical scaffolds were optimized for activity yielding compound ML390, and genetic resistance and sequencing efforts identified dihydroorotate dehydrogenase (DHODH) as the target enzyme. The DHODH inhibitor brequinar works against these leukemic cells as well. The X-ray crystal structure of ML390 bound to DHODH elucidates ML390s binding interactions.

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Organizational Affiliation: 
• Center for the Science of Therapeutics, Broad Institute , Cambridge, Massachusetts 02142, United States.
Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, United States; Cancer Center, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.
Center for the Science of Therapeutics, Broad Institute, Cambridge, Massachusetts 02142, United States; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States.
School of Pharmaceutical Sciences, University of São Paulo , Ribeirão Preto, São Paulo 14040-903, Brazil.
Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, United States; Cancer Center, Massachusetts General Hospital, Boston, Massachusetts 02114, United States; Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, United States; Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, United States.
Center for the Science of Therapeutics, Broad Institute, Cambridge, Massachusetts 02142, United States; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States; Howard Hughes Medical Institute, Cambridge, Massachusetts 02138, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.71 kDa 
• Atom Count: 3,287 
• Modeled Residue Count: 359 
• Deposited Residue Count: 368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase (quinone), mitochondrial	A	368	Homo sapiens	Mutation(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 GTEx:  ENSG00000102967

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CE9	D [auth A]	DODECYL NONA ETHYLENE GLYCOL ETHER C30 H62 O10 ONJQDTZCDSESIW-UHFFFAOYSA-N
FNR	B [auth A]	1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL C17 H23 N4 O9 P YTNIXZGTHTVJBW-SCRDCRAPSA-N
ORO	C [auth A]	OROTIC ACID C5 H4 N2 O4 PXQPEWDEAKTCGB-UHFFFAOYSA-N
SO4	E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	M [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	G [auth A], H [auth A], I [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	J [auth A], K [auth A], L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.160 (Depositor), 0.163 (DCC) 
• R-Value Work:  0.136 (Depositor), 0.139 (DCC) 
• R-Value Observed: 0.138 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.14	α = 90
b = 90.14	β = 90
c = 122.152	γ = 120

Software Package:

Software Name	Purpose
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-12 
Deposition Author(s): Lewis, T.A., Sykes, D.B., Law, J.M., Munoz, B., Scadden, D.T., Rustiguel, J.K., Nonato, M.C., Schreiber, S.L.

Revision History  

• Version 1.0: 2016-10-12
  Type: Initial release
  
• Version 1.1: 2017-01-04
  Changes: Database references
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description