Crystal structure of the EGFR kinase domain in complex with 4-(4-{[2-{[(3S)-1-acetylpyrrolidin-3-yl]amino}-9-(propan-2-yl)-9H-purin-6-yl]amino}phenyl)-1-methylpiperazin-1-ium

Experimental Data Snapshot

  • Resolution: 2.53 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Discovery of N-((3R,4R)-4-Fluoro-1-(6-((3-methoxy-1-methyl-1H-pyrazol-4-yl)amino)-9-methyl-9H-purin-2-yl)pyrrolidine-3-yl)acrylamide (PF-06747775) through Structure-Based Drug Design: A High Affinity Irreversible Inhibitor Targeting Oncogenic EGFR Mutants with Selectivity over Wild-Type EGFR.

Planken, S.Behenna, D.C.Nair, S.K.Johnson, T.O.Nagata, A.Almaden, C.Bailey, S.Ballard, T.E.Bernier, L.Cheng, H.Cho-Schultz, S.Dalvie, D.Deal, J.G.Dinh, D.M.Edwards, M.P.Ferre, R.A.Gajiwala, K.S.Hemkens, M.Kania, R.S.Kath, J.C.Matthews, J.Murray, B.W.Niessen, S.Orr, S.T.Pairish, M.Sach, N.W.Shen, H.Shi, M.Solowiej, J.Tran, K.Tseng, E.Vicini, P.Wang, Y.Weinrich, S.L.Zhou, R.Zientek, M.Liu, L.Luo, Y.Xin, S.Zhang, C.Lafontaine, J.

(2017) J Med Chem 60: 3002-3019

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b01894
  • Primary Citation of Related Structures:  
    5UG8, 5UG9, 5UGA, 5UGB, 5UGC

  • PubMed Abstract: 

    Mutant epidermal growth factor receptor (EGFR) is a major driver of non-small-cell lung cancer (NSCLC). Marketed first generation inhibitors, such as erlotinib, effect a transient beneficial response in EGFR mutant NSCLC patients before resistance mechanisms render these inhibitors ineffective. Secondary oncogenic EGFR mutations account for approximately 50% of relapses, the most common being the gatekeeper T790M substitution that renders existing therapies ineffective. The discovery of PF-06459988 (1), an irreversible pyrrolopyrimidine inhibitor of EGFR T790M mutants, was recently disclosed.1 Herein, we describe our continued efforts to achieve potency across EGFR oncogenic mutations and improved kinome selectivity, resulting in the discovery of clinical candidate PF-06747775 (21), which provides potent EGFR activity against the four common mutants (exon 19 deletion (Del), L858R, and double mutants T790M/L858R and T790M/Del), selectivity over wild-type EGFR, and desirable ADME properties. Compound 21 is currently being evaluated in phase-I clinical trials of mutant EGFR driven NSCLC.

  • Organizational Affiliation

    Wuxi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor329Homo sapiensMutation(s): 0 
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 8BM

Download Ideal Coordinates CCD File 
B [auth A]4-(4-{[2-{[(3S)-1-acetylpyrrolidin-3-yl]amino}-9-(propan-2-yl)-9H-purin-6-yl]amino}phenyl)-1-methylpiperazin-1-ium
C25 H35 N9 O
Binding Affinity Annotations 
IDSourceBinding Affinity
8BM BindingDB:  5UGB Ki: 161 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.53 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.706α = 90
b = 146.706β = 90
c = 146.706γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-04-26
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references