7D5O | pdb_00007d5o

C-Src in complex with TAS-120

• PDB DOI: https://doi.org/10.2210/pdb7D5O/pdb

• Classification: TRANSFERASE
• Organism(s): Gallus gallus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-09-27 Released: 2021-12-22 
• Deposition Author(s): Qu, L.Z., Chen, Y.H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 
  0.237 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Structural insights into the potency and selectivity of covalent pan-FGFR inhibitors

Qu, L., Chen, X., Wei, H., Guo, M., Dai, S., Jiang, L., Li, J., Yue, S., Chen, Z., Chen, Y.

(2022) Commun Chem 5: 5

• DOI: https://doi.org/10.1038/s42004-021-00623-x

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 66.29 kDa 
• Atom Count: 4,094 
• Modeled Residue Count: 501 
• 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 [auth B], B [auth A]	286	Gallus gallus	Mutation(s): 0  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
TZ0 (Subject of Investigation/LOI)	C [auth B], D [auth A]	1-[(3S)-3-{4-amino-3-[(3,5-dimethoxyphenyl)ethynyl]-1H-pyrazolo[3,4-d]pyrimidin-1-yl}pyrrolidin-1-yl]prop-2-en-1-one C22 H22 N6 O3 KEIPNCCJPRMIAX-HNNXBMFYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free:  0.237 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.969	α = 100.64
b = 63.184	β = 90.61
c = 73.137	γ = 89.82

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-12-22 
Deposition Author(s): Qu, L.Z., Chen, Y.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81570537
National Natural Science Foundation of China (NSFC)	China	81974074
National Natural Science Foundation of China (NSFC)	China	31900880

Revision History  

• Version 1.0: 2021-12-22
  Type: Initial release
  
• Version 2.0: 2022-02-09
  Type: Coordinate replacement
  Reason: Ligand identity
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2022-03-09
  Changes: Database references
• Version 2.2: 2023-11-29
  Changes: Data collection, Refinement description