6P69 | pdb_00006p69

Crystal structure of FGFR1-Y563C (FGFR4 surrogate) covalently bound to compound 11.

• PDB DOI: https://doi.org/10.2210/pdb6P69/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-06-03 Released: 2019-06-19 
• Deposition Author(s): Larsen, N.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.245 (Depositor) 
• R-Value Work: 
  0.186 (Depositor) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

To be published

Prajapati, S.

(null) Tbd 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 71.91 kDa 
• Atom Count: 4,936 
• Modeled Residue Count: 574 
• Deposited Residue Count: 618 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibroblast growth factor receptor 1	A, B	309	Homo sapiens	Mutation(s): 2  Gene Names: FGFR1, BFGFR, CEK, FGFBR, FLG, FLT2, HBGFR EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11362 (Homo sapiens) Explore P11362  Go to UniProtKB:  P11362
PHAROS:  P11362 GTEx:  ENSG00000077782

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O21 (Subject of Investigation/LOI)	F [auth A], J [auth B]	N-{2-[(6-{[(2,6-dichloro-3,5-dimethoxyphenyl)carbamoyl][3-(4-methylpiperazin-1-yl)propyl]amino}pyrimidin-4-yl)amino]phenyl}prop-2-enamide C30 H36 Cl2 N8 O4 QBUHMHIIROCODG-UHFFFAOYSA-N
SO4	C [auth A], G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	D [auth A], E [auth A], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
O21	BindingDB:  6P69	IC50: 1020 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.245 (Depositor) 
• R-Value Work:  0.186 (Depositor) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 205.365	α = 90
b = 58.516	β = 107.31
c = 66.131	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-06-19 
Deposition Author(s): Larsen, N.A.

Revision History  

• Version 1.0: 2019-06-19
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary