5SYS | pdb_00005sys

c-Src V281C bound to N-[3-({6-[(1E)-2-cyano-3-(methylamino)-3-oxoprop-1-en-1-yl]-7-(2-methoxyethyl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl}ethynyl)-4-methylphenyl]-3-(trifluoromethyl)benzamide inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5SYS/pdb

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


• Deposited: 2016-08-11 Released: 2017-08-16 
• Deposition Author(s): Dieter, E.M., Merritt, E.A., Maly, D.J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.334 (Depositor), 0.332 (DCC) 
• R-Value Work: 
  0.286 (Depositor), 0.289 (DCC) 
• R-Value Observed: 
  0.288 (Depositor) 

Starting Model: experimental

Literature

A combined approach reveals a regulatory mechanism coupling Src's kinase activity, localization, and phosphotransferase-independent functions

Register, A.C., Maly, D.J.

(null) Mol Cell 2019

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 66.64 kDa 
• Atom Count: 4,297 
• Modeled Residue Count: 516 
• Deposited Residue Count: 572 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase Src	A, B	286	Gallus gallus	Mutation(s): 1  Gene Names: SRC EC: 2.7.10.2
UniProt
Find proteins for P00523 (Gallus gallus) Explore P00523  Go to UniProtKB:  P00523

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
72F	C [auth A], D [auth B]	N-[3-({6-[(2S)-2-cyano-3-(methylamino)-3-oxopropyl]-7-(2-methoxyethyl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl}ethynyl)-4-methylphenyl]-3-(trifluoromethyl)benzamide C31 H27 F3 N6 O3 JDCJZTAGQPRSAO-QFIPXVFZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.334 (Depositor), 0.332 (DCC) 
• R-Value Work:  0.286 (Depositor), 0.289 (DCC) 
• R-Value Observed: 0.288 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.813	α = 77.87
b = 63.857	β = 90.1
c = 75.625	γ = 89.83

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-08-16 
Deposition Author(s): Dieter, E.M., Merritt, E.A., Maly, D.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM086858

Revision History  

• Version 1.0: 2017-08-16
  Type: Initial release
  
• Version 1.1: 2018-01-17
  Changes: Author supporting evidence
• Version 1.2: 2019-02-27
  Changes: Data collection, Database references
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-11-06
  Changes: Structure summary