6LP8 | pdb_00006lp8

Crystal structure of human DHODH in complex with inhibitor 1243


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 
    0.174 (Depositor), 0.176 (DCC) 
  • R-Value Work: 
    0.157 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.157 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6LP8

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Bifunctional Naphtho[2,3- d ][1,2,3]triazole-4,9-dione Compounds Exhibit Antitumor Effects In Vitro and In Vivo by Inhibiting Dihydroorotate Dehydrogenase and Inducing Reactive Oxygen Species Production.

Zuo, Z.Liu, X.Qian, X.Zeng, T.Sang, N.Liu, H.Zhou, Y.Tao, L.Zhou, X.Su, N.Yu, Y.Chen, Q.Luo, Y.Zhao, Y.

(2020) J Med Chem 63: 7633-7652

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00512
  • Primary Citation Related Structures: 
    6JMD, 6JME, 6LP6, 6LP7, 6LP8

  • PubMed Abstract: 

    Human dihydroorotate dehydrogenase ( h DHODH) is an attractive target for cancer therapy. Based on its crystal structure, we designed and synthesized a focused compound library containing the structural moiety of 1,4-benzoquinone, which possesses reactive oxygen species (ROS) induction capacity. Compound 3s with a naphtho[2,3- d ][1,2,3]triazole-4,9-dione scaffold exhibited inhibitory activity against h DHODH. Further optimization led to compounds 11k and 11l , which inhibited h DHODH activity with IC 50 values of 9 and 4.5 nM, respectively. Protein-ligand cocrystal structures clearly depicted hydrogen bond and hydrophobic interactions of 11k and 11l with h DHODH. Compounds 11k and 11l significantly inhibited leukemia cell and solid tumor cell proliferation and induced ROS production, mitochondrial dysfunction, apoptosis, and cell cycle arrest. Nanocrystallization of compound 11l displayed significant in vivo antitumor effects in the Raji xenograft model. Overall, this study provides a novel bifunctional compound 11l with h DHODH inhibition and ROS induction efficacy, which represents a promising anticancer lead worthy of further exploration.


  • Organizational Affiliation
    • State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China.

Macromolecule Content 

  • Total Structure Weight: 41.55 kDa 
  • Atom Count: 3,222 
  • Modeled Residue Count: 365 
  • Deposited Residue Count: 366 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dihydroorotate dehydrogenase (quinone), mitochondrial366Homo 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
B [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
B6O
(Subject of Investigation/LOI)

Query on B6O



Download:Ideal Coordinates CCD File
J [auth A]3-[4-[3-(dimethylamino)phenyl]-3,5-bis(fluoranyl)phenyl]benzo[f]benzotriazole-4,9-dione
C24 H16 F2 N4 O2
DIQAKQHNMJSKDT-UHFFFAOYSA-N
LDA

Query on LDA



Download:Ideal Coordinates CCD File
H [auth A]LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
ORO

Query on ORO



Download:Ideal Coordinates CCD File
C [auth A]OROTIC ACID
C5 H4 N2 O4
PXQPEWDEAKTCGB-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ACT

Query on ACT



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
I [auth A],
K [auth A],
L [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
M [auth A],
N [auth A],
O [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free:  0.174 (Depositor), 0.176 (DCC) 
  • R-Value Work:  0.157 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.157 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.558α = 90
b = 90.558β = 90
c = 122.427γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description