Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.27 kDa 
• Atom Count: 2397 
• Modelled Residue Count: 283 
• Deposited Residue Count: 298 
• Unique protein chains: 1

1DI8

THE STRUCTURE OF CYCLIN-DEPENDENT KINASE 2 (CDK2) IN COMPLEX WITH 4-[3-HYDROXYANILINO]-6,7-DIMETHOXYQUINAZOLINE

• DOI: 10.2210/pdb1DI8/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 1999-11-29 Released: 2000-11-29 
• Deposition Author(s): Shewchuk, L., Hassell, A., Kuyper, L.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.226 
• R-Value Work: 0.186 

Literature

Binding mode of the 4-anilinoquinazoline class of protein kinase inhibitor: X-ray crystallographic studies of 4-anilinoquinazolines bound to cyclin-dependent kinase 2 and p38 kinase.

Shewchuk, L., Hassell, A., Wisely, B., Rocque, W., Holmes, W., Veal, J., Kuyper, L.F.

(2000) J Med Chem 43: 133-138

• PubMed: 10633045 
• DOI: 10.1021/jm990401t
• Primary Citation of Related Structures:  
  1DI9, 1DI8


• PubMed Abstract: 
  

4-Anilinoquinazolines represent an important class of protein kinase inhibitor. Modes of binding for two members of this inhibitor class were determined by X-ray crystallographic analysis of one inhibitor (4-[3-hydroxyanilino]-6,7-dimethoxyquinazoline) in complex with cyclin-dependent kinase 2 (CDK2) and the other (4-[3-methylsulfanylanilino]-6,7-dimethoxyquinazoline) in complex with p38 kinase. In both inhibitor/kinase structures, the 4-anilinoquinazoline was bound in the ATP site with the quinazoline ring system oriented along the peptide strand that links the two domains of the protein and with the anilino substituent projecting into a hydrophobic pocket within the protein interior. In each case, the nitrogen at position-1 of the quinazoline accepted a hydrogen bond from a backbone NH (CDK2, Leu-83; p38, Met-109) of the domain connector strand, and aromatic hydrogen atoms at C2 and C8 interacted with backbone carbonyl oxygen atoms of the peptide strand. The anilino group of the CDK2-bound compound was essentially coplanar with the quinazoline ring system and occupied a pocket between Lys-33 and Phe-80. For the p38-bound inhibitor, the anilino group was angled out of plane and was positioned between Lys-53 and Thr-106 in a manner similar to that observed for the aryl substituent of the pyridinylimidazole class of inhibitor.

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Organizational Affiliation: 

Glaxo Wellcome Inc., Five Moore Drive, Research Triangle Park, North Carolina 27709, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLIN-DEPENDENT KINASE 2	A	298	Homo sapiens	Mutation(s): 0  Gene Names: CDK2, CDKN2 EC: 2.7.1 (PDB Primary Data), 2.7.11.22 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens) Explore P24941  Go to UniProtKB:  P24941
PHAROS:  P24941 GTEx:  ENSG00000123374

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTQ	B [auth A]	4-[3-HYDROXYANILINO]-6,7-DIMETHOXYQUINAZOLINE C16 H15 N3 O3 BNDYIYYKEIXHNK-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DTQ	IC50 :  1000   nM  PDBBind
DTQ	IC50:  1000   nM  BindingDB
DTQ	IC50:  1000   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.226 
• R-Value Work: 0.186 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.752	α = 90
b = 74.076	β = 90
c = 54.005	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-11-29 
• Released Date: 2000-11-29 
Deposition Author(s): Shewchuk, L., Hassell, A., Kuyper, L.F.

Revision History  

• Version 1.0: 2000-11-29
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance