8GB4

EGFR(T790M/V948R) kinase in complex with benzimidazole allosteric inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

EGFR(T790M/V948R) kinase in complex with benzimidazole allosteric inhibitor

Beyett, T.S.Eck, M.J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor
A, B, C, D
331Homo sapiensMutation(s): 2 
Gene Names: EGFRERBBERBB1HER1
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00533
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YW5 (Subject of Investigation/LOI)
Query on YW5

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C],
P [auth D]
2-[(R)-(1H-benzimidazol-2-yl)(3-fluorophenyl)methyl]-6-[4-(1-methylpiperidin-4-yl)phenyl]-2,3-dihydro-1H-isoindol-1-one
C34 H31 F N4 O
ZMKPSKAUYOLPIA-JGCGQSQUSA-N
ANP
Query on ANP

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
O [auth D]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
N [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.45α = 90
b = 73.45β = 118.45
c = 118.419γ = 90
Software Package:
Software NamePurpose
DIALSdata scaling
PHENIXrefinement
DIALSdata reduction
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States5R01CA116020-16
National Institutes of Health/National Cancer Institute (NIH/NCI)United States5R01CA201049-08

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-13
    Type: Initial release