3OUJ

PHD2 with 2-Oxoglutarate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


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

  • DOI: https://doi.org/10.1021/ml100198y
  • Primary Citation of 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 ...

    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.

    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Egl nine homolog 1237Homo sapiensMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9GZT9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AKG
Query on AKG
Download Ideal Coordinates CCD File 
D [auth A]2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
FE2
Query on FE2
Download Ideal Coordinates CCD File 
C [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
AKG PDBBind:  3OUJ Kd: 900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.298α = 90
b = 72.298β = 90
c = 46.496γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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