2Z8C

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

• PDB DOI: https://doi.org/10.2210/pdb2Z8C/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2007-09-05 Released: 2008-08-12 
• Deposition Author(s): Katayama, N., Kurihara, H.

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Experimental Data Snapshot

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

Starting Model: experimental

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

• PubMed: 18767165 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.83 kDa 
• Atom Count: 2,466 
• Modelled Residue Count: 306 
• Deposited Residue Count: 309 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin receptor	A	303	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
6-mer peptide from Insulin receptor substrate 1	B	6	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S91	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
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

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 = 71.54	α = 90
b = 71.54	β = 90
c = 133.85	γ = 120

Software Package:

Software Name	Purpose
CNX	refinement
MOSFLM	data reduction
SCALA	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-12 
Deposition Author(s): Katayama, N., Kurihara, H.

Revision History  

• 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
• Version 1.6: 2024-11-20
  Changes: Structure summary