8Y0V

HIF prolyl hydroxylase 2 in complex with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8Y0V/pdb

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


• Deposited: 2024-01-23 Released: 2024-12-18 
• Deposition Author(s): Ding, X., Fan, Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.291 (Depositor), 0.297 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.228 (DCC) 

Starting Model: experimental

Literature

Intestinal mucosal barrier repair and immune regulation with an AI-developed gut-restricted PHD inhibitor.

Fu, Y., Ding, X., Zhang, M., Feng, C., Yan, Z., Wang, F., Xu, J., Lin, X., Ding, X., Wang, L., Fan, Y., Li, T., Yin, Y., Liang, X., Xu, C., Chen, S., Pulous, F.E., Gennert, D., Pun, F.W., Kamya, P., Ren, F., Aliper, A., Zhavoronkov, A.

(2024) Nat Biotechnol 

• PubMed: 39663371 
• DOI: https://doi.org/10.1038/s41587-024-02503-w
• Primary Citation of Related Structures:  
  8Y0V


• PubMed Abstract: 
  

  Hypoxia-inducible factor prolyl hydroxylase (PHD) inhibitors have been approved for treating renal anemia yet have failed clinical testing for inflammatory bowel disease because of a lack of efficacy. Here we used a multimodel multimodal generative artificial intelligence platform to design an orally gut-restricted selective PHD1 and PHD2 inhibitor that exhibits favorable safety and pharmacokinetic profiles in preclinical studies. ISM012-042 restores intestinal barrier function and alleviates gut inflammation in multiple experimental colitis models.

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Organizational Affiliation: 

Insilico Medicine US, Inc., Boston, MA, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 28.07 kDa 
• Atom Count: 1,634 
• Modelled Residue Count: 197 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Egl nine homolog 1	A	246	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
A1D5X (Subject of Investigation/LOI)	B [auth A]	~{tert}-butyl 4-[6-[(6-cyanopyridin-3-yl)methylcarbamoyl]-5-oxidanyl-1,7-naphthyridin-2-yl]piperazine-1-carboxylate C25 H27 N7 O4 VXVKDBNSYJRFIQ-UHFFFAOYSA-N
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.291 (Depositor), 0.297 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.228 (DCC) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.415	α = 90
b = 82.415	β = 90
c = 63.472	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-18 
Deposition Author(s): Ding, X., Fan, Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-12-18
  Type: Initial release
  
• Version 1.1: 2024-12-25
  Changes: Database references