6AGX | pdb_00006agx

The cocrystal structure of FGFR2 bound with compound 14 harboring 5H-pyrrolo[2,3-b]pyrazine scaffold

• PDB DOI: https://doi.org/10.2210/pdb6AGX/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2018-08-15 Released: 2019-08-21 
• Deposition Author(s): Xiong, B.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.298 (Depositor), 0.301 (DCC) 
• R-Value Work: 
  0.251 (Depositor), 0.253 (DCC) 
• R-Value Observed: 
  0.254 (Depositor) 

Starting Model: experimental

Literature

The cocrystal structure of FGFR2 bound with compound 14 harboring 5H-pyrrolo[2,3-b]pyrazine scaffold

Xiong, B.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 140.2 kDa 
• Atom Count: 9,544 
• Modeled Residue Count: 1,165 
• Deposited Residue Count: 1,192 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibroblast growth factor receptor 2	A, B, C, D	298	Homo sapiens	Mutation(s): 1  Gene Names: FGFR2 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P21802 (Homo sapiens) Explore P21802  Go to UniProtKB:  P21802
PHAROS:  P21802 GTEx:  ENSG00000066468

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9WX	E [auth A], F [auth B], G [auth C], H [auth D]	ethyl [4-({3-[2-(3,5-dimethoxyphenyl)ethyl]-5H-pyrrolo[2,3-b]pyrazin-5-yl}sulfonyl)-1H-imidazol-1-yl]acetate C23 H25 N5 O6 S GMHRLLCUAFMSGQ-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.298 (Depositor), 0.301 (DCC) 
• R-Value Work:  0.251 (Depositor), 0.253 (DCC) 
• R-Value Observed: 0.254 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.317	α = 90
b = 78.27	β = 96.47
c = 99.251	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-08-21 
Deposition Author(s): Xiong, B.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	XDA12020317

Revision History  

• Version 1.0: 2019-08-21
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary