9I4H | pdb_00009i4h

Factor Inhibiting HIF (FIH) in complex with manganese and 3-Hydroxy-5-(3-(4-(hydroxymethyl)-3-nitrophenyl)isoxazol-5-yl)picolinoyl)glycine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.218 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9I4H

Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history

Literature

Light-Induced, Lysine-Targeting Irreversible Covalent Inhibition of the Human Oxygen Sensing Hydroxylase Factor Inhibiting HIF (FIH).

Wu, Y.Li, Z.Kaur, S.Zhang, Z.Yue, J.Tumber, A.Zhang, H.Song, Z.Yang, P.Dong, Y.Yang, F.Li, X.Schofield, C.J.Zhang, X.

(2025) J Am Chem Soc 147: 17871-17879

  • DOI: https://doi.org/10.1021/jacs.5c01935
  • Primary Citation Related Structures: 
    9I4H

  • PubMed Abstract: 

    Factor inhibiting hypoxia-inducible factor (FIH) is a JmjC domain 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase that catalyzes protein hydroxylations, including of specific asparagines in the C -terminal transcriptional activation domains of hypoxia-inducible factor alpha (HIF-α) isoforms. FIH is of medicinal interest due to its ability to alter metabolism and modulate the course of the HIF-mediated hypoxic response. We report the development of a light-induced, lysine (Lys106)-targeting irreversible covalent inhibitor of FIH. The approach is complementary to optogenetic methods for regulation of transcription. The covalently reacting inhibitor NBA-ZG-2291 was the result of structure-guided modification of the reported active site binding FIH inhibitor ZG-2291 with an appropriately positioned o -nitrobenzyl alcohol ( o -NBA) group. The results demonstrate that NBA-ZG-2291 forms a stable covalent bond in a light-dependent process with Lys106 of FIH, inactivating its hydroxylation activity and resulting in sustained upregulation of FIH-dependent HIF target genes. The light-controlled inhibitors targeting a lysine residue enable light and spatiotemporal control of FIH activity in a manner useful for dissecting the context-dependent physiological roles of FIH.


  • Organizational Affiliation
    • State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, and Department of Chemistry, China Pharmaceutical University, Nanjing 211198, China.

Macromolecule Content 

  • Total Structure Weight: 40.88 kDa 
  • Atom Count: 2,871 
  • Modeled Residue Count: 335 
  • Deposited Residue Count: 350 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hypoxia-inducible factor 1-alpha inhibitor350Homo sapiensMutation(s): 0 
Gene Names: HIF1ANFIH1
EC: 1.14.11.30 (PDB Primary Data), 1.14.11 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWT6 (Homo sapiens)
Explore Q9NWT6 
Go to UniProtKB:  Q9NWT6
PHAROS:  Q9NWT6
GTEx:  ENSG00000166135 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NWT6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IZ5
(Subject of Investigation/LOI)

Query on A1IZ5



Download:Ideal Coordinates CCD File
C [auth A]N-[(5P)-3-hydroxy-5-{(3P)-3-[4-(hydroxymethyl)-3-nitrophenyl]-1,2-oxazol-5-yl}pyridine-2-carbonyl]glycine
C18 H14 N4 O8
HJSCSBRLOWROBA-UHFFFAOYSA-N
MN

Query on MN



Download:Ideal Coordinates CCD File
B [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.218 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.028α = 90
b = 86.028β = 90
c = 147.495γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/L009846/1
National Natural Science Foundation of China (NSFC)ChinaNo. 82322062 (Medicinal chemistry)

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release
  • Version 1.1: 2025-06-11
    Changes: Database references
  • Version 2.0: 2026-04-15
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary