6J3B

Crystal structure of human DHODH in complex with inhibitor 1289


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

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Ligand Structure Quality Assessment 


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Literature

A novel series of human dihydroorotate dehydrogenase inhibitors discovered by in vitro screening: inhibition activity and crystallographic binding mode.

Zeng, T.Zuo, Z.Luo, Y.Zhao, Y.Yu, Y.Chen, Q.

(2019) FEBS Open Bio 9: 1348-1354

  • DOI: 10.1002/2211-5463.12658
  • Primary Citation of Related Structures:  
    6J3B, 6J3C

  • PubMed Abstract: 
  • Human dihydroorotate dehydrogenase (DHODH), the enzyme that catalyzes the rate-limiting step in de novo pyrimidine biosynthesis, is considered to be an attractive target for potential treatment of autoimmune disease and cancer. Here, we present a novel class of human DHODH inhibitors with high inhibitory potency ...

    Human dihydroorotate dehydrogenase (DHODH), the enzyme that catalyzes the rate-limiting step in de novo pyrimidine biosynthesis, is considered to be an attractive target for potential treatment of autoimmune disease and cancer. Here, we present a novel class of human DHODH inhibitors with high inhibitory potency. The high-resolution crystal structures of human DHODH complexed with various agents reveal the details of their interactions. Comparisons with the binding modes of teriflunomide and brequinar provide insights that may facilitate the development of new inhibitors targeting human DHODH.


    Organizational Affiliation

    Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dihydroorotate dehydrogenase (quinone), mitochondrialA366Homo 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
D [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
B5O (Subject of Investigation/LOI)
Query on B5O

Download Ideal Coordinates CCD File 
F [auth A](6R)-1-[3,5-bis(fluoranyl)-4-[2-fluoranyl-5-(hydroxymethyl)phenyl]phenyl]-6-propan-2-yl-6,7-dihydro-5H-benzotriazol-4-one
C22 H20 F3 N3 O2
PDEIRWICIYOXPB-CYBMUJFWSA-N
 Ligand Interaction
LDA (Subject of Investigation/LOI)
Query on LDA

Download Ideal Coordinates CCD File 
G [auth A]LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
ORO (Subject of Investigation/LOI)
Query on ORO

Download Ideal Coordinates CCD File 
E [auth A]OROTIC ACID
C5 H4 N2 O4
PXQPEWDEAKTCGB-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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B [auth A], C [auth A], P [auth A], Q [auth A], R [auth A], S [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
DMS
Query on DMS

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H [auth A], I [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
T [auth A], U [auth A], V [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
W [auth A], X [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
B5O Binding MOAD:  6J3B IC50: 171 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.829α = 90
b = 90.829β = 90
c = 122.754γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2019-01-04 
  • Released Date: 2019-08-21 
  • Deposition Author(s): Yu, Y., Chen, Q.

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-21
    Type: Initial release