CRYSTAL STRUCTURE OF VEGFR2 (JUXTAMEMBRANE AND KINASE DOMAINS) IN COMPLEX WITH AXITINIB (AG-013736) (N-Methyl-2-(3-((E)-2-pyridin-2-yl- vinyl)-1H-indazol-6-ylsulfanyl)-benzamide)

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.204 

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This is version 1.3 of the entry. See complete history


Molecular Conformations, Interactions, and Properties Associated with Drug Efficiency and Clinical Performance Among Vegfr Tk Inhibitors.

Mctigue, M.Murray, B.W.Chen, J.H.Deng, Y.Solowiej, J.Kania, R.S.

(2012) Proc Natl Acad Sci U S A 109: 18281

  • DOI: https://doi.org/10.1073/pnas.1207759109
  • Primary Citation of Related Structures:  
    4AG8, 4AGC, 4AGD, 4ASD, 4ASE

  • PubMed Abstract: 

    Analyses of compounds in clinical development have shown that ligand efficient-molecules with privileged physical properties and low dose are less likely to fail in the various stages of clinical testing, have fewer postapproval withdrawals, and are less likely to receive black box safety warnings. However, detailed side-by-side examination of molecular interactions and properties within single drug classes are lacking. As a class, VEGF receptor tyrosine kinase inhibitors (VEGFR TKIs) have changed the landscape of how cancer is treated, particularly in clear cell renal cell carcinoma, which is molecularly linked to the VEGF signaling axis. Despite the clear role of the molecular target, member molecules of this validated drug class exhibit distinct clinical efficacy and safety profiles in comparable renal cell carcinoma clinical studies. The first head-to-head randomized phase III comparative study between active VEGFR TKIs has confirmed significant differences in clinical performance [Rini BI, et al. (2011) Lancet 378:193-1939]. To elucidate how fundamental drug potency-efficiency is achieved and impacts differentiation within the VEGFR TKI class, we determined potencies, time dependence, selectivities, and X-ray structures of the drug-kinase complexes using a VEGFR2 TK construct inclusive of the important juxtamembrane domain. Collectively, the studies elucidate unique drug-kinase interactions that are dependent on distinct juxtamembrane domain conformations, resulting in significant potency and ligand efficiency differences. The identified structural trends are consistent with in vitro measurements, which translate well to clinical performance, underscoring a principle that may be broadly applicable to prospective drug design for optimal in vivo performance.

  • Organizational Affiliation

    Department of Oncology Medicinal Chemistry, Pfizer Worldwide Research and Development, Pfizer Inc., San Diego, CA 92121, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UniProt & NIH Common Fund Data Resources
Find proteins for P35968 (Homo sapiens)
Explore P35968 
Go to UniProtKB:  P35968
PHAROS:  P35968
GTEx:  ENSG00000128052 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35968
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on AXI

Download Ideal Coordinates CCD File 
C22 H18 N4 O S
Binding Affinity Annotations 
IDSourceBinding Affinity
AXI PDBBind:  4AGC Ki: 0.02 (nM) from 1 assay(s)
Binding MOAD:  4AGC Ki: 0.02 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.492α = 90
b = 56.922β = 97.12
c = 50.787γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-26
    Type: Initial release
  • Version 1.1: 2012-11-14
    Changes: Database references
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description