5ZTO

Crystal structure of EGFR 696-1022 T790M/C797S in complex with D3003

• PDB DOI: https://doi.org/10.2210/pdb5ZTO/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2018-05-04 Released: 2019-06-12 
• Deposition Author(s): Zhu, S.J., Yun, C.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.272 
• R-Value Work: 0.231 
• R-Value Observed: 0.234 

Starting Model: experimental

Literature

Crystal structure of EGFR 696-1022 T790M/C797S in complex with D3003

Zhu, S.J., Yun, C.H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 38.29 kDa 
• Atom Count: 2,351 
• Modelled Residue Count: 294 
• Deposited Residue Count: 331 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A	331	Homo sapiens	Mutation(s): 2  Gene Names: EGFR, ERBB, ERBB1, HER1 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00533 (Homo sapiens) Explore P00533  Go to UniProtKB:  P00533
PHAROS:  P00533 GTEx:  ENSG00000146648

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9JO	B [auth A]	N-{trans-4-[3-(2-chlorophenyl)-7-{[3-methyl-4-(4-methylpiperazin-1-yl)phenyl]amino}-2-oxo-3,4-dihydropyrimido[4,5-d]pyrimidin-1(2H)-yl]cyclohexyl}propanamide C33 H41 Cl N8 O2 WVLWGBZNXIVAKC-YOCNBXQISA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
9JO	BindingDB:  5ZTO	IC50: min: 5.8, max: 31 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.272 
• R-Value Work: 0.231 
• R-Value Observed: 0.234 
• Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.731	α = 90
b = 148.731	β = 90
c = 148.731	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-06-12 
Deposition Author(s): Zhu, S.J., Yun, C.H.

Revision History  

• Version 1.0: 2019-06-12
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description