9H46 | pdb_00009h46

EGFR wild type in complex with 25328

PDB DOI: https://doi.org/10.2210/pdb9H46/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-10-17 Released: 2024-12-04
Deposition Author(s): Pintar, S., Martin, M.P., Noble, M.E.M.
Funding Organization(s): Cancer Research UK, Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.16 Å
R-Value Free:
0.256 (Depositor), 0.253 (DCC)
R-Value Work:
0.212 (Depositor), 0.213 (DCC)

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

Covalent alkynylpyridopyrimidinones targeting cysteine 775 of the epidermal growth factor receptor overcome resistance to current therapies

Stewart, H.L., Waring, M.J.

To be published.

Macromolecule Content

Total Structure Weight: 37.81 kDa
Atom Count: 2,422
Modeled Residue Count: 305
Deposited Residue Count: 328
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A	328	Homo sapiens	Mutation(s): 0 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00533
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1ISA (Subject of Investigation/LOI) Query on A1ISA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	5-ethyl-2-[(2-methoxyphenyl)amino]-8-phenyl-pyrido[2,3-d]pyrimidin-7-one C₂₂ H₂₀ N₄ O₂ HPXXVKFIRJYEBH-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.16 Å
R-Value Free: 0.256 (Depositor), 0.253 (DCC)
R-Value Work: 0.212 (Depositor), 0.213 (DCC)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.696	α = 90
b = 144.696	β = 90
c = 144.696	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-12-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	DRCDDRPGMApr2020100002
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/X004872/1

Revision History (Full details and data files)

Version 1.0: 2024-12-04
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.