5HZN

Structure of NVP-AEW541 in complex with IGF-1R kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Identification of a 5-[3-phenyl-(2-cyclic-ether)-methylether]-4-aminopyrrolo[2,3-d]pyrimidine series of IGF-1R inhibitors.

Stauffer, F.Cowan-Jacob, S.W.Scheufler, C.Furet, P.

(2016) Bioorg Med Chem Lett 26: 2065-2067

  • DOI: https://doi.org/10.1016/j.bmcl.2016.02.074
  • Primary Citation of Related Structures:  
    5HHW, 5HZN

  • PubMed Abstract: 

    We report structure-guided modifications of the benzyloxy substituent of the Insulin-like Growth Factor-1 Receptor (IGF-1R) inhibitor NVP-AEW541. This chemical group has been shown to confer selectivity against other protein kinases but at the expense of a metabolism liability. X-ray crystallography has revealed that the benzyloxy moiety interacts with a lysine cation of the IGF-1R kinase domain via its ether function and its aromatic π-system and is nicely embedded in an induced hydrophobic pocket. We show that 1,4-diethers displaying an adequate hydrophobic and constrained shape are advantageous benzyloxy replacements. A single digit nanomolar inhibitor (compound 20, IC50=8.9 nM) was identified following this approach.


  • Organizational Affiliation

    Novartis Institutes for Biomedical Research, Basel, Postfach, 4002 Basel, Switzerland. Electronic address: frederic.stauffer@novartis.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Insulin-like growth factor 1 receptor
A, B, C, D, E
A, B, C, D, E, F, G, H
304Homo sapiensMutation(s): 2 
Gene Names: IGF1R
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P08069 (Homo sapiens)
Explore P08069 
Go to UniProtKB:  P08069
GTEx:  ENSG00000140443 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08069
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
66A
Query on 66A

Download Ideal Coordinates CCD File 
AA [auth H]
I [auth A]
L [auth B]
N [auth C]
Q [auth D]
AA [auth H],
I [auth A],
L [auth B],
N [auth C],
Q [auth D],
S [auth E],
V [auth F],
X [auth G]
7-[cis-3-(azetidin-1-ylmethyl)cyclobutyl]-5-[3-(benzyloxy)phenyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine
C27 H29 N5 O
AECDBHGVIIRMOI-GRGXKFILSA-N
MES
Query on MES

Download Ideal Coordinates CCD File 
BA [auth H]
J [auth A]
M [auth B]
O [auth C]
R [auth D]
BA [auth H],
J [auth A],
M [auth B],
O [auth C],
R [auth D],
T [auth E],
W [auth F],
Y [auth G]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
K [auth A],
P [auth C],
U [auth E],
Z [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
66A BindingDB:  5HZN IC50: min: 20, max: 65 (nM) from 4 assay(s)
Binding MOAD:  5HZN IC50: 61 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.435α = 90
b = 190.045β = 90.22
c = 155.488γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2016-12-21
    Changes: Refinement description