1PF8

Crystal Structure of Human Cyclin-Dependent Kinase 2 Complexed with a Nucleoside Inhibitor

• PDB DOI:  https://doi.org/10.2210/pdb1PF8/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2003-05-24 Released: 2003-12-23 
• Deposition Author(s): Moshinsky, D.J., Bellamacina, R.C., Boisvert, D.C., Huang, P., Hui, T., Jancarik, J., Kim, S.H., Rice, A.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.306 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 

Literature

SU9516: biochemical analysis of cdk inhibition and crystal structure in complex with cdk2.

Moshinsky, D.J., Bellamacina, C.R., Boisvert, D.C., Huang, P., Hui, T., Jancarik, J., Kim, S.H., Rice, A.G.

(2003) Biochem Biophys Res Commun 310: 1026-1031

• PubMed: 14550307 
• DOI: https://doi.org/10.1016/j.bbrc.2003.09.114
• Primary Citation of Related Structures:  
  1PF8


• PubMed Abstract: 
  

SU9516 is a 3-substituted indolinone compound with demonstrated potent and selective inhibition toward cyclin dependent kinases (cdks). Here, we describe the kinetic characterization of this inhibition with respect to cdk2, 1, and 4, along with the crystal structure in complex with cdk2. The molecule is competitive with respect to ATP for cdk2/cyclin A, with a K(i) value of 0.031 microM. Similarly, SU9516 inhibits cdk2/cyclin E and cdk1/cyclin B1 in an ATP-competitive manner, although at a 2- to 8-fold reduced potency. In contrast, the compound exhibited non-competitive inhibition with respect to ATP toward cdk4/cyclin D1, with a 45-fold reduced potency. The X-ray crystal structure of SU9516 bound to cdk2 revealed interactions between the molecule and Leu83 and Glu81 of the kinase. This study should aid in the development of more potent and selective cdk inhibitors for potential therapeutic agents.

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Organizational Affiliation: 

SUGEN, Inc., South San Francisco, CA 94080, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.22 kDa 
• Atom Count: 2,415 
• Modelled Residue Count: 298 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division protein kinase 2	A	298	Homo sapiens	Mutation(s): 0  Gene Names: CDK2, CDKN2 EC: 2.7.1.37 (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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SU9	B [auth A]	(3Z)-3-(1H-IMIDAZOL-5-YLMETHYLENE)-5-METHOXY-1H-INDOL-2(3H)-ONE C13 H11 N3 O2 QNUKRWAIZMBVCU-WCIBSUBMSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SU9	PDBBind:  1PF8	Ki: 31 (nM) from 1 assay(s)
	BindingDB:  1PF8	IC50: min: 22, max: 110 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.306 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.753	α = 90
b = 72.306	β = 90
c = 71.944	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
GLRF	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-12-23 
Deposition Author(s): Moshinsky, D.J., Bellamacina, R.C., Boisvert, D.C., Huang, P., Hui, T., Jancarik, J., Kim, S.H., Rice, A.G.

Revision History  

• Version 1.0: 2003-12-23
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2014-04-16
  Changes: Data collection
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description