3OUJ | pdb_00003ouj

PHD2 with 2-Oxoglutarate

• PDB DOI: https://doi.org/10.2210/pdb3OUJ/pdb

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


• Deposited: 2010-09-14 Released: 2010-12-01 
• Deposition Author(s): Staker, B.L., Arakaki, T.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.253 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

Benzimidazole-2-pyrazole HIF Prolyl 4-Hydroxylase Inhibitors as Oral Erythropoietin Secretagogues.

Rosen, M.D., Venkatesan, H., Peltier, H.M., Bembenek, S.D., Kanelakis, K.C., Zhao, L.X., Leonard, B.E., Hocutt, F.M., Wu, X., Palomino, H.L., Brondstetter, T.I., Haugh, P.V., Cagnon, L., Yan, W., Liotta, L.A., Young, A., Mirzadegan, T., Shankley, N.P., Barrett, T.D., Rabinowitz, M.H.

(2010) ACS Med Chem Lett 1: 526-529

• PubMed: 24900242 
• DOI: https://doi.org/10.1021/ml100198y
• Primary Citation Related Structures: 
  3OUH, 3OUI, 3OUJ


• PubMed Abstract: 
  

  HIF prolyl 4-hydroxylases (PHD) are a family of enzymes that mediate key physiological responses to hypoxia by modulating the levels of hypoxia inducible factor 1-α (HIF1α). Certain benzimidazole-2-pyrazole carboxylates were discovered to be PHD2 inhibitors using ligand- and structure-based methods and found to be potent, orally efficacious stimulators of erythropoietin secretion in vivo.

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Organizational Affiliation: 
• Johnson & Johnson Pharmaceutical Research and Development, L.L.C, 3210 Merryfield Row, San Diego, California 92121, United States.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 26.88 kDa 
• Atom Count: 1,856 
• Modeled Residue Count: 226 
• Deposited Residue Count: 237 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Egl nine homolog 1	A	237	Homo sapiens	Mutation(s): 0  Gene Names: EGLN1, C1orf12, PNAS-118, PNAS-137 EC: 1.14.11 (PDB Primary Data), 1.14.11.29 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZT9 (Homo sapiens) Explore Q9GZT9  Go to UniProtKB:  Q9GZT9
PHAROS:  Q9GZT9 GTEx:  ENSG00000135766

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKG	D [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
FE2	C [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.253 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.298	α = 90
b = 72.298	β = 90
c = 46.496	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-01 
Deposition Author(s): Staker, B.L., Arakaki, T.L.

Revision History  

• Version 1.0: 2010-12-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-04-18
  Changes: Data collection, Database references
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations