8J1K | pdb_00008j1k

co-crystal structure of non-carboxylic acid inhibitor with PHD2

• PDB DOI: https://doi.org/10.2210/pdb8J1K/pdb

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


• Deposited: 2023-04-13 Released: 2024-04-17 
• Deposition Author(s): Xu, J., Fu, Y., Ding, X., Meng, Q., Wang, L., Zhang, M., Ding, X., Ren, F., Zhavoronkov, A.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.308 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.240 (DCC) 

Starting Model: experimental

Literature

co-crystal structure of non-carboxylic acid inhibitor with PHD2

Xu, J., Fu, Y., Ding, X., Meng, Q., Wang, L., Man, Z., Ding, X., Ren, F., Zhavoronkov, A.

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 24.94 kDa 
• Atom Count: 1,629 
• Modeled Residue Count: 198 
• Deposited Residue Count: 218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Egl nine homolog 1	A	218	Homo sapiens	Mutation(s): 0  Gene Names: EGLN1, C1orf12, PNAS-118, PNAS-137 EC: 1.14.11.29
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
SY6 (Subject of Investigation/LOI)	B [auth A]	N-[(6-cyanopyridin-3-yl)methyl]-5-oxidanyl-2-[(3R)-3-oxidanylpyrrolidin-1-yl]-1,7-naphthyridine-6-carboxamide C20 H18 N6 O3 ROTOKWNRJPNVEV-CQSZACIVSA-N
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.308 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.240 (DCC) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.843	α = 90
b = 80.843	β = 90
c = 63.899	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-17 
Deposition Author(s): Xu, J., Fu, Y., Ding, X., Meng, Q., Wang, L., Zhang, M., Ding, X., Ren, F., Zhavoronkov, A.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2024-04-17
  Type: Initial release