2HBU | pdb_00002hbu

Crystal structure of HIF prolyl hydroxylase EGLN-1 in complex with a biologically active inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2HBU/pdb

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


• Deposited: 2006-06-14 Released: 2006-06-27 
• Deposition Author(s): Evdokimov, A.G., Walter, R.L., Mekel, M., Pokross, M.E., Kawamoto, R., Boyer, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.231 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of HIF prolyl hydroxylase in complex with a biologically active inhibitor

Evdokimov, A.G., Walter, R.L., Mekel, M., Pokross, M.E., Kawamoto, R., Boyer, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.17 kDa 
• Atom Count: 1,964 
• Modeled Residue Count: 219 
• Deposited Residue Count: 247 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Egl nine homolog 1	A	247	Homo sapiens	Mutation(s): 0  Gene Names: EGLN1 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UN9	C [auth A]	N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE C12 H9 Cl N2 O4 OUQVKRKGTAUJQA-UHFFFAOYSA-N
FE2	B [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
UN9	BindingDB:  2HBU	Kd: 80 (nM) from 1 assay(s)
		IC50: min: 70, max: 7500 (nM) from 8 assay(s)
		EC50: 7.90e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.231 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.045	α = 90
b = 111.045	β = 90
c = 40.126	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-27 
Deposition Author(s): Evdokimov, A.G., Walter, R.L., Mekel, M., Pokross, M.E., Kawamoto, R., Boyer, A.

Revision History  

• Version 1.0: 2006-06-27
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description