2Z8C

Phosphorylated insulin receptor tyrosine kinase in complex with (4-{[5-carbamoyl-4-(3-methylanilino)pyrimidin-2-yl]amino}phenyl)acetic acid

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.217 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history. 


Literature

Identification of a key element for hydrogen-bonding patterns between protein kinases and their inhibitors.

Katayama, N., Orita, M., Yamaguchi, T., Hisamichi, H., Kuromitsu, S., Kurihara, H., Sakashita, H., Matsumoto, Y., Fujita, S., Niimi, T.

(2008) Proteins 73: 795-801

  • DOI: https://doi.org/10.1002/prot.22207
  • Primary Citation of Related Structures:  
    2Z7L, 2Z8C

  • PubMed Abstract: 

    In this article, we report crystal structures for inhibitor-kinase complexes in which the inhibitor has different binding orientations and hydrogen-bonding patterns with extracellular-signal regulated kinase 2 and insulin receptor tyrosine kinase. Our crystallographic studies, and sequence and structural analyses of 532 coordinates of kinases held in the Protein Data Bank, suggest that the length of the "specificity linker" described here is a key structural element of the hydrogen-bonding patterns between protein kinases and their inhibitors.

    • Organizational Affiliation: 

    Drug Discovery Research, Astellas Pharma Inc., 21 Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Insulin receptor303Homo sapiensMutation(s): 2 
Gene Names: INSR
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P06213 (Homo sapiens)
Explore P06213 
Go to UniProtKB:  P06213
PHAROS:  P06213
GTEx:  ENSG00000171105 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06213
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
6-mer peptide from Insulin receptor substrate 16Homo sapiensMutation(s): 0 
Gene Names: IRS1
UniProt & NIH Common Fund Data Resources
Find proteins for P35568 (Homo sapiens)
Explore P35568 
Go to UniProtKB:  P35568
PHAROS:  P35568
GTEx:  ENSG00000169047 
Entity Groups  
UniProt GroupP35568
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
S91
Query on S91
Download Ideal Coordinates CCD File 
C [auth A][4-({5-(AMINOCARBONYL)-4-[(3-METHYLPHENYL)AMINO]PYRIMIDIN-2-YL}AMINO)PHENYL]ACETIC ACID
C20 H19 N5 O3
PAIQRYUOBBCBSE-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.217 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.54α = 90
b = 71.54β = 90
c = 133.85γ = 120
Software Package:
Software NamePurpose
CNXrefinement
MOSFLMdata reduction
SCALAdata scaling
CNXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-11
    Changes: Refinement description
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-11-01
    Changes: Data collection, Refinement description
  • Version 1.5: 2023-11-15
    Changes: Data collection