8Z32 | pdb_00008z32

Crystal Structure of HIF-PHD2 in complex with compound 3

• PDB DOI: https://doi.org/10.2210/pdb8Z32/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-04-14 Released: 2025-02-26 
• Deposition Author(s): Ito, S., Baba, D., Fukuda, T., Tanaka, N.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.245 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Discovery of DS44470011: An oral hypoxia-inducible factor prolyl hydroxylase inhibitor for the treatment of renal anemia.

Fukuda, T., Kuribayashi, T., Takano, R., Sasaki, K., Tsuji, T., Niitsu, Y., Ishii, K., Hashimoto, M., Baba, D., Ito, S., Tanaka, N.

(2024) Bioorg Med Chem Lett 108: 129799-129799

• PubMed: 38754564 
• DOI: https://doi.org/10.1016/j.bmcl.2024.129799
• Primary Citation Related Structures: 
  8Z31, 8Z32, 8Z33, 8Z35


• PubMed Abstract: 
  

  Inhibition of the hypoxia-inducible factor prolyl hydroxylase (HIF-PHD) represents a promising strategy for discovering next-generation treatments for renal anemia. We identified a pyrimidine core with HIF-PHD inhibitory activity based on scaffold hopping of FG-2216 using crystal structures of HIF-PHD2 in complex with compound. By optimizing the substituents at the 2- and 6- positions of the pyrimidine core, we discovered DS44470011, which improves the effectiveness of erythropoietin (EPO) release in cells. Oral administration of DS44470011 to cynomolgus monkeys increased plasma EPO levels.

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Organizational Affiliation: 
• R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan. Electronic address: [e-mail].
R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.42 kDa 
• Atom Count: 3,403 
• Modeled Residue Count: 416 
• Deposited Residue Count: 494 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Egl nine homolog 1	A, B	247	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
A1L0V (Subject of Investigation/LOI)	D [auth A], F [auth B]	2-[[6-[(4-fluorophenyl)methyl]-2-methyl-5-oxidanyl-pyrimidin-4-yl]carbonylamino]ethanoic acid C15 H14 F N3 O4 MNJZVYOQKXSJCJ-UHFFFAOYSA-N
FE2	C [auth A], E [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.245 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.43	α = 90
b = 67.743	β = 116.36
c = 67.272	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-02-26 
Deposition Author(s): Ito, S., Baba, D., Fukuda, T., Tanaka, N.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-02-26
  Type: Initial release