6ET4

HUMAN DIHYDROOROTATE DEHYDROGENASE IN COMPLEX WITH NOVEL INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.105 
  • R-Value Observed: 0.107 

wwPDB Validation 3D Report Full Report



Literature

A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage.

Ladds, M.J.G.W.van Leeuwen, I.M.M.Drummond, C.J.Chu, S.Healy, A.R.Popova, G.Pastor Fernandez, A.Mollick, T.Darekar, S.Sedimbi, S.K.Nekulova, M.Sachweh, M.C.C.Campbell, J.Higgins, M.Tuck, C.Popa, M.Safont, M.M.Gelebart, P.Fandalyuk, Z.Thompson, A.M.Svensson, R.Gustavsson, A.L.Johansson, L.Farnegardh, K.Yngve, U.Saleh, A.Haraldsson, M.D'Hollander, A.C.A.Franco, M.Zhao, Y.Hakansson, M.Walse, B.Larsson, K.Peat, E.M.Pelechano, V.Lunec, J.Vojtesek, B.Carmena, M.Earnshaw, W.C.McCarthy, A.R.Westwood, N.J.Arsenian-Henriksson, M.Lane, D.P.Bhatia, R.McCormack, E.Lain, S.

(2018) Nat Commun 9: 1107-1107

  • DOI: 10.1038/s41467-018-03441-3
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The development of non-genotoxic therapies that activate wild-type p53 in tumors is of great interest since the discovery of p53 as a tumor suppressor. Here we report the identification of over 100 small-molecules activating p53 in cells. We elucidat ...

    The development of non-genotoxic therapies that activate wild-type p53 in tumors is of great interest since the discovery of p53 as a tumor suppressor. Here we report the identification of over 100 small-molecules activating p53 in cells. We elucidate the mechanism of action of a chiral tetrahydroindazole (HZ00), and through target deconvolution, we deduce that its active enantiomer (R)-HZ00, inhibits dihydroorotate dehydrogenase (DHODH). The chiral specificity of HZ05, a more potent analog, is revealed by the crystal structure of the (R)-HZ05/DHODH complex. Twelve other DHODH inhibitor chemotypes are detailed among the p53 activators, which identifies DHODH as a frequent target for structurally diverse compounds. We observe that HZ compounds accumulate cancer cells in S-phase, increase p53 synthesis, and synergize with an inhibitor of p53 degradation to reduce tumor growth in vivo. We, therefore, propose a strategy to promote cancer cell killing by p53 instead of its reversible cell cycle arresting effect.


    Organizational Affiliation

    SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden. sonia.lain@ki.se.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydroorotate dehydrogenase (quinone), mitochondrialA367Homo sapiensMutation(s): 0 
Gene Names: DHODH
EC: 1.3.5.2
Find proteins for Q02127 (Homo sapiens)
Explore Q02127 
Go to UniProtKB:  Q02127
NIH Common Fund Data Resources
PHAROS  Q02127
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download CCD File 
A
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
SDV
Query on SDV

Download CCD File 
A
N-[(4R)-1-(2-fluorophenyl)-4,5,6,7-tetrahydroindazol-4-yl]-2,1-benzoxazole-3-carboxamide
C21 H17 F N4 O2
KVYFUACEMBMTLM-MRXNPFEDSA-N
 Ligand Interaction
DDQ
Query on DDQ

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

Download CCD File 
A
(4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID
C5 H6 N2 O4
UFIVEPVSAGBUSI-REOHCLBHSA-N
 Ligand Interaction
SO4
Query on SO4

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

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download CCD File 
A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SDVIC50:  11   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.105 
  • R-Value Observed: 0.107 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.86α = 90
b = 90.86β = 90
c = 122.7γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-03-28
    Type: Initial release