6SYP | pdb_00006syp

Human DHODH bound to inhibitor IPP/CNRS-A017

• PDB DOI: https://doi.org/10.2210/pdb6SYP/pdb

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


• Deposited: 2019-09-30 Released: 2019-10-09 
• Deposition Author(s): Kraemer, A., Janin, Y., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.203 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.190 (DCC) 

Starting Model: experimental

Literature

IPP/CNRS-A017: A chemical probe for human dihydroorotate dehydrogenase (hDHODH)

Kramer, A., Tjaden, A., Ndreshkjana, B., Tredup, C., Farin, H.F., Knapp, S., Janin, Y.L., Muller, S.

(2022) Curr Res Chem Biol 2: 100034

• DOI: https://doi.org/10.1016/j.crchbi.2022.100034

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 44.04 kDa 
• Atom Count: 2,846 
• Modeled Residue Count: 347 
• Deposited Residue Count: 395 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase	A [auth AAA]	395	Homo sapiens	Mutation(s): 0  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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth AAA]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
M0B (Subject of Investigation/LOI)	E [auth AAA]	2-[4-[2,6-bis(fluoranyl)phenoxy]-5-methyl-3-propan-2-yloxy-pyrazol-1-yl]-5-cyclopropyl-3-fluoranyl-pyridine C21 H20 F3 N3 O2 JNAABFZPXJJMPX-UHFFFAOYSA-N
ORO	C [auth AAA]	OROTIC ACID C5 H4 N2 O4 PXQPEWDEAKTCGB-UHFFFAOYSA-N
SO4	D [auth AAA]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
M0B	BindingDB:  6SYP	IC50: 25 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.203 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.190 (DCC) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.565	α = 90
b = 90.565	β = 90
c = 122.387	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-09 
Deposition Author(s): Kraemer, A., Janin, Y., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2019-10-09
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2024-01-24
  Changes: Refinement description
• Version 1.3: 2024-12-04
  Changes: Database references, Structure summary