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

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:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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

View Full Validation Report

Ligand Structure Quality Assessment

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

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.