5K9C

Crystal structure of human dihydroorotate dehydrogenase with ML390


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.131 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1021/acsmedchemlett.6b00316
  • Primary Citation of Related Structures:  

  • 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 d ...

    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.


    Organizational Affiliation

    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; Howard Hughes Medical Institute, Cambridge, Massachusetts 02138, United States.,School of Pharmaceutical Sciences, University of São Paulo , Ribeirão Preto, São Paulo 14040-903, Brazil.,Center for the Science of Therapeutics, Broad Institute , Cambridge, Massachusetts 02142, 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.,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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydroorotate dehydrogenase (quinone), mitochondrial
A
368Homo 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 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLJ
Query on MLJ

Download SDF File 
Download CCD File 
A
~{N}-[3-oxidanylidene-3-[[(1~{R})-1,2,3,4-tetrahydronaphthalen-1-yl]amino]propyl]-4-(trifluoromethyloxy)benzamide
C21 H21 F3 N2 O3
SGNRHEDBLPGDDC-GOSISDBHSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

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

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FNR
Query on FNR

Download SDF File 
Download CCD File 
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
TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE
C17 H23 N4 O9 P
YTNIXZGTHTVJBW-SCRDCRAPSA-N
 Ligand Interaction
ORO
Query on ORO

Download SDF File 
Download CCD File 
A
OROTIC ACID
C5 H4 N2 O4
PXQPEWDEAKTCGB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LJIC50: 560 nM (100) BINDINGDB
MLJIC50: 560 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.131 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 89.900α = 90.00
b = 89.900β = 90.00
c = 121.771γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-10-12
    Type: Initial release
  • Version 1.1: 2017-01-04
    Type: Database references