8JN8 | pdb_00008jn8

Crystal structure of c-Src in complex with covalent inhibitor DC-Srci-6668

PDB DOI: https://doi.org/10.2210/pdb8JN8/pdb

Classification: ONCOPROTEIN/INHIBITOR
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2023-06-06 Released: 2024-06-12
Deposition Author(s): Zhang, H.M., Luo, C.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.254 (Depositor), 0.250 (DCC)
R-Value Work:
0.210 (Depositor), 0.210 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The crystal structure of c-Src in complex with covalent inhibitor DC-Srci-6668

Zhang, H.M., Luo, C.

To be published.

Macromolecule Content

Total Structure Weight: 60.3 kDa
Atom Count: 3,981
Modeled Residue Count: 451
Deposited Residue Count: 536
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase Src	A	536	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
JA6 (Subject of Investigation/LOI) Query on JA6 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]	(2R)-N-cyclopentyl-2-[cyclopropyl(ethanoyl)amino]-2-(4-fluorophenyl)ethanamide C₁₈ H₂₃ F N₂ O₂ WMTNJDDVDAMKPW-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

Binding Affinity Annotations
ID	Source	Binding Affinity
PTR	BindingDB: 8JN8	-TΔS: -1.81e+1 (kJ/mol) from 1 assay(s)
PTR	BindingDB: 8JN8	ΔG: -2.14e+1 (kJ/mol) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.254 (Depositor), 0.250 (DCC)
R-Value Work: 0.210 (Depositor), 0.210 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.189	α = 90
b = 82.91	β = 90
c = 106.623	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-06-12

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2024-06-12
Type: Initial release
Version 1.1: 2024-11-13
Changes: Structure summary

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.