8K4F

DHODH in complex with compound A0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Discovery and Optimization of Novel h DHODH Inhibitors for the Treatment of Inflammatory Bowel Disease.

Zhou, X.Gou, K.Xu, J.Jian, L.Luo, Y.Li, C.Guan, X.Qiu, J.Zou, J.Zhang, Y.Zhong, X.Zeng, T.Zhou, Y.Xiao, Y.Yang, X.Chen, W.Gao, P.Liu, C.Zhou, Y.Tao, L.Liu, X.Cen, X.Chen, Q.Sun, Q.Luo, Y.Zhao, Y.

(2023) J Med Chem 66: 14755-14786

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01365
  • Primary Citation of Related Structures:  
    8K4F

  • PubMed Abstract: 

    As a key rate-limiting enzyme in the de novo synthesis of pyrimidine nucleotides, human dihydroorotate dehydrogenase ( h DHODH) is considered a known target for the treatment of autoimmune diseases, including inflammatory bowel disease (IBD). Herein, BAY 41-2272 with a 1 H -pyrazolo[3,4- b ]pyridine scaffold was identified as an h DHODH inhibitor by screening an active compound library containing 5091 molecules. Further optimization led to 2-(1-(2-chloro-6-fluorobenzyl)-1 H -pyrrolo[2,3- b ]pyridin-3-yl)-5-cyclopropylpyrimidin-4-amine ( w2) , which was found to be the most promising and drug-like compound with potent inhibitory activity against h DHODH (IC 50 = 173.4 nM). Compound w2 demonstrated acceptable pharmacokinetic characteristics and alleviated the severity of acute ulcerative colitis induced by dextran sulfate sodium in a dose-dependent manner. Notably, w2 exerted better therapeutic effects on ulcerative colitis than h DHODH inhibitor vidofludimus and Janus kinase (JAK) inhibitor tofacitinib. Taken together, w2 is a promising h DHODH inhibitor for the treatment of IBD and deserves to be developed as a preclinical candidate.


  • Organizational Affiliation

    Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence 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
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 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
D [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
FJW (Subject of Investigation/LOI)
Query on FJW

Download Ideal Coordinates CCD File 
N [auth A]5-cyclopropyl-2-[1-[(2-fluorophenyl)methyl]pyrazolo[3,4-b]pyridin-3-yl]pyrimidin-4-amine
C20 H17 F N6
ATOAHNRJAXSBOR-UHFFFAOYSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
C [auth A],
M [auth A]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
OG6
Query on OG6

Download Ideal Coordinates CCD File 
E [auth A]6-[bis(oxidanyl)methyl]-5~{H}-pyrimidine-2,4-dione
C5 H6 N2 O4
DUGHQFVNXIWPEA-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
I [auth A],
L [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ACT
Query on ACT

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.261α = 90
b = 91.261β = 90
c = 123.005γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data scaling
HKL-3000data reduction
HKL-3000phasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82273850

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-29
    Type: Initial release