6M2B | pdb_00006m2b

Crystal structure of human dihydroorotate dehydrogenase (DHODH) with S416


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 
    0.193 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.169 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Novel and potent inhibitors targeting DHODH are broad-spectrum antivirals against RNA viruses including newly-emerged coronavirus SARS-CoV-2.

Xiong, R.Zhang, L.Li, S.Sun, Y.Ding, M.Wang, Y.Zhao, Y.Wu, Y.Shang, W.Jiang, X.Shan, J.Shen, Z.Tong, Y.Xu, L.Chen, Y.Liu, Y.Zou, G.Lavillete, D.Zhao, Z.Wang, R.Zhu, L.Xiao, G.Lan, K.Li, H.Xu, K.

(2020) Protein Cell 11: 723-739

  • DOI: https://doi.org/10.1007/s13238-020-00768-w
  • Primary Citation Related Structures: 
    6M2B

  • PubMed Abstract: 

    Emerging and re-emerging RNA viruses occasionally cause epidemics and pandemics worldwide, such as the on-going outbreak of the novel coronavirus SARS-CoV-2. Herein, we identified two potent inhibitors of human DHODH, S312 and S416, with favorable drug-likeness and pharmacokinetic profiles, which all showed broad-spectrum antiviral effects against various RNA viruses, including influenza A virus, Zika virus, Ebola virus, and particularly against SARS-CoV-2. Notably, S416 is reported to be the most potent inhibitor so far with an EC 50 of 17 nmol/L and an SI value of 10,505.88 in infected cells. Our results are the first to validate that DHODH is an attractive host target through high antiviral efficacy in vivo and low virus replication in DHODH knock-out cells. This work demonstrates that both S312/S416 and old drugs (Leflunomide/Teriflunomide) with dual actions of antiviral and immuno-regulation may have clinical potentials to cure SARS-CoV-2 or other RNA viruses circulating worldwide, no matter such viruses are mutated or not.


  • Organizational Affiliation
    • Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.

Macromolecule Content 

  • Total Structure Weight: 43.62 kDa 
  • Atom Count: 3,059 
  • Modeled Residue Count: 365 
  • Deposited Residue Count: 390 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dihydroorotate dehydrogenase (quinone), mitochondrial390Homo 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
GTEx:  ENSG00000102967 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02127
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / 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
EZO
(Subject of Investigation/LOI)

Query on EZO



Download:Ideal Coordinates CCD File
D [auth A]2-[(E)-[[4-(2-chlorophenyl)-1,3-thiazol-2-yl]-methyl-hydrazinylidene]methyl]benzoic acid
C18 H14 Cl N3 O2 S
MWIQPUXVXAVFRM-KEBDBYFISA-N
ORO

Query on ORO



Download:Ideal Coordinates CCD File
C [auth A]OROTIC ACID
C5 H4 N2 O4
PXQPEWDEAKTCGB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free:  0.193 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.04α = 90
b = 91.04β = 90
c = 122.18γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2021-03-03 
  • Deposition Author(s): Zhu, L., Li, H.

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-03
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-29
    Changes: Refinement description