6LZL

Crystal structure of human dihydroorotate dehydrogenase (DHODH) with Piperine

• PDB DOI: https://doi.org/10.2210/pdb6LZL/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2020-02-19 Released: 2020-04-15 
• Deposition Author(s): Liu, Z.H., Wu, D., Lu, W.Q., Huang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.209 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 

Literature

Crystal structure of human dihydroorotate dehydrogenase (DHODH) with Piperine

Liu, Z.H., Wu, D., Lu, W.Q., Huang, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content

• Total Structure Weight: 40.55 kDa 
• Atom Count: 2,928 
• Modelled Residue Count: 364 
• Deposited Residue Count: 365 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase (quinone), mitochondrial	A	365	Homo sapiens	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	C [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
AYR (Subject of Investigation/LOI)	D [auth A]	(2E,4E)-5-(2H-1,3-benzodioxol-5-yl)-1-(piperidin-1-yl)penta-2,4-dien-1-one C17 H19 N O3 MXXWOMGUGJBKIW-YPCIICBESA-N
ORO	B [auth A]	OROTIC ACID C5 H4 N2 O4 PXQPEWDEAKTCGB-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AYR	BindingDB:  6LZL	Ki: 710 (nM) from 1 assay(s)
		IC50: 880 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.209 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.413	α = 90
b = 90.413	β = 90
c = 122.699	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-15 
Deposition Author(s): Liu, Z.H., Wu, D., Lu, W.Q., Huang, J.

Revision History  

• Version 1.0: 2020-04-15
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references