9D5E | pdb_00009d5e

Crystal structure of the ILK/alpha-parvin core complex bound to gefitinib

• PDB DOI: https://doi.org/10.2210/pdb9D5E/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-08-13 Released: 2025-10-29 
• Deposition Author(s): Fukuda, K., Qin, J.
• Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the ILK/alpha-parvin core complex bound to gefitinib

Fukuda, K., Qin, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 46.99 kDa 
• Atom Count: 3,637 
• Modeled Residue Count: 395 
• Deposited Residue Count: 400 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin-linked protein kinase	A	271	Homo sapiens	Mutation(s): 2  Gene Names: ILK, ILK1, ILK2 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13418 (Homo sapiens) Explore Q13418  Go to UniProtKB:  Q13418
PHAROS:  Q13418 GTEx:  ENSG00000166333

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-parvin	B	129	Homo sapiens	Mutation(s): 0  Gene Names: PARVA, MXRA2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NVD7 (Homo sapiens) Explore Q9NVD7  Go to UniProtKB:  Q9NVD7
PHAROS:  Q9NVD7 GTEx:  ENSG00000197702

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IRE (Subject of Investigation/LOI)	C [auth A], D [auth A]	Gefitinib C22 H24 Cl F N4 O3 XGALLCVXEZPNRQ-UHFFFAOYSA-N
B3P (Subject of Investigation/LOI)	E [auth B]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C11 H26 N2 O6 HHKZCCWKTZRCCL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.26	α = 90
b = 118.418	β = 101.161
c = 47.606	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Fukuda, K., Qin, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	2R01HL058758-23A1

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release