2Z7L | pdb_00002z7l

Unphosphorylated Mitogen Activated Protein Kinase ERK2 in Complex with (4-{[5-Carbamoyl-4-(3-Methylanilino)Pyrimidin 2-Yl]Amino}Phenyl)Acetic Acid

• PDB DOI: https://doi.org/10.2210/pdb2Z7L/pdb

• Classification: TRANSFERASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-08-27 Released: 2008-08-12 
• Deposition Author(s): Katayama, N., Kurihara, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 
  0.276 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.219 (DCC) 

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 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: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 43.07 kDa 
• Atom Count: 2,864 
• Modeled Residue Count: 329 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 1	A	366	Rattus norvegicus	Mutation(s): 0  Gene Names: Mapk1, Erk2, Mapk, Prkm1 EC: 2.7.11.24
UniProt
Find proteins for P63086 (Rattus norvegicus) Explore P63086  Go to UniProtKB:  P63086

Small Molecules

Ligands 3 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
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BME	D [auth A], E [auth A], F [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.276 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.219 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.873	α = 90
b = 69.962	β = 109.58
c = 60.775	γ = 90

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: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description