4WKQ

1.85 angstrom structure of EGFR kinase domain with gefitinib

PDB DOI: https://doi.org/10.2210/pdb4WKQ/pdb

Classification: transferase/transferase inhibitor
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2014-10-03 Released: 2014-11-05
Deposition Author(s): Yosaatmadja, Y., Squire, C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.225
R-Value Work: 0.194
R-Value Observed: 0.196

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

1.85 angstrom structure of EGFR kinase domain with gefitinib

Yosaatmadja, Y., Squire, C.J., McKeage, M., Flanagan, J.U.

To be published.

Macromolecule Content

Total Structure Weight: 38.24 kDa
Atom Count: 2,503
Modelled Residue Count: 297
Deposited Residue Count: 330
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A	330	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IRE Query on IRE 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]	Gefitinib C₂₂ H₂₄ Cl F N₄ O₃ XGALLCVXEZPNRQ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSX Query on CSX	A	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.225
R-Value Work: 0.194
R-Value Observed: 0.196
Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.714	α = 90
b = 143.714	β = 90
c = 143.714	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-11-05

Deposition Author(s):

Yosaatmadja, Y.

Squire, C.J.

Revision History (Full details and data files)

Version 1.0: 2014-11-05
Type: Initial release
Version 1.1: 2015-02-04
Changes: Derived calculations
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
Version 1.3: 2024-03-27
Changes: Data collection

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Help and Resources

4WKQ

1.85 angstrom structure of EGFR kinase domain with gefitinib

1.85 angstrom structure of EGFR kinase domain with gefitinib

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)