6ET4

HUMAN DIHYDROOROTATE DEHYDROGENASE IN COMPLEX WITH NOVEL INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.105 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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

  • 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

    Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydroorotate dehydrogenase (quinone), mitochondrial
A
367Homo 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 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FMN
Query on FMN

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A
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
SDV
Query on SDV

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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
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DOR
Query on DOR

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A
(4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID
DIHYDROOROTIC ACID
C5 H6 N2 O4
UFIVEPVSAGBUSI-REOHCLBHSA-N
 Ligand Interaction
DDQ
Query on DDQ

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A
DECYLAMINE-N,N-DIMETHYL-N-OXIDE
C12 H27 N O
ZRKZFNZPJKEWPC-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

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A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.105 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 90.860α = 90.00
b = 90.860β = 90.00
c = 122.700γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
Aimlessdata scaling
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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