9IRL | pdb_00009irl

Crystal structure analysis of LW-Srci-2o in complex with c-Src.

PDB DOI: https://doi.org/10.2210/pdb9IRL/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2024-07-16 Released: 2025-07-16
Deposition Author(s): Xu, D., Huiming, Z., Hongchan, H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free:
0.243 (Depositor), 0.244 (DCC)
R-Value Work:
0.187 (Depositor), 0.188 (DCC)
R-Value Observed:
0.189 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 9IRL

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure-based development of selective covalent inhibitors targeting a dynamic allosteric pocket of c-Src kinase

Xu, D.

To be published.

Macromolecule Content

Total Structure Weight: 51.96 kDa
Atom Count: 3,864
Modeled Residue Count: 451
Deposited Residue Count: 451
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase Src	A	451	Homo sapiens	Mutation(s): 0 Gene Names: SRC, SRC1 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P12931 (Homo sapiens) Explore P12931 Go to UniProtKB: P12931
PHAROS: P12931 GTEx: ENSG00000197122
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12931
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1L20 (Subject of Investigation/LOI) Query on A1L20 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(2~{R})-2-[3,5-bis(fluoranyl)phenyl]-2-[2-chloranylethanoyl(cyclopropyl)amino]-~{N}-cyclopentyl-ethanamide C₁₈ H₂₁ Cl F₂ N₂ O₂ QCBHBBUSQYJKAT-QGZVFWFLSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR Query on PTR	A	L-PEPTIDE LINKING	C₉ H₁₂ N O₆ P		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.243 (Depositor), 0.244 (DCC)
R-Value Work: 0.187 (Depositor), 0.188 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.114	α = 90
b = 85.134	β = 90
c = 107.361	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-16

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81821005

Revision History (Full details and data files)

Version 1.0: 2025-07-16
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.