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 

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Ligand Structure Quality Assessment 


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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: https://doi.org/10.1038/s41467-018-03441-3
  • Primary Citation of Related Structures:  
    6ET4

  • 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 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 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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dihydroorotate dehydrogenase (quinone), mitochondrial367Homo sapiensMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02127
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN
Download Ideal Coordinates CCD File 
B [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N		 Ligand Interaction
SDV
Query on SDV
Download Ideal Coordinates CCD File 
D [auth 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 Ideal Coordinates CCD File 
E [auth A]DECYLAMINE-N,N-DIMETHYL-N-OXIDE
C12 H27 N O
ZRKZFNZPJKEWPC-UHFFFAOYSA-N		 Ligand Interaction
DOR
Query on DOR
Download Ideal Coordinates CCD File 
C [auth A](4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID
C5 H6 N2 O4
UFIVEPVSAGBUSI-REOHCLBHSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
M [auth A],
N [auth A]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
L [auth A]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
ACY
Query on ACY
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth A]		ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
O [auth A],
P [auth A],
Q [auth A]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
SDV Binding MOAD:  6ET4 IC50: 11 (nM) from 1 assay(s)
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

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

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