1YKR | pdb_00001ykr

Crystal structure of cdk2 with an aminoimidazo pyridine inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1YKR/pdb

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


• Deposited: 2005-01-18 Released: 2006-01-24 
• Deposition Author(s): Hamdouchi, C., Zhong, B., Mendoza, J., Jaramillo, C., Zhang, F., Brooks, H.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.271 (Depositor) 
• R-Value Work: 
  0.255 (Depositor) 
• R-Value Observed: 
  0.260 (Depositor) 

Starting Model: experimental

Literature

Structure-based design of a new class of highly selective aminoimidazo[1,2-a]pyridine-based inhibitors of cyclin dependent kinases

Hamdouchi, C., Zhong, B., Mendoza, J., Collins, E., Jaramillo, C., De Diego, J.E., Robertson, D., Spencer, C.D., Anderson, B.D., Watkins, S.A., Zhang, F., Brooks, H.B.

(2005) Bioorg Med Chem Lett 15: 1943-1947

• PubMed: 15780638 
• DOI: https://doi.org/10.1016/j.bmcl.2005.01.052
• Primary Citation Related Structures: 
  1YKR


• PubMed Abstract: 
  

  Structure-based design approach was successfully used to guide the evolution of imidazopyridine scaffold yielding new structural class of highly selective inhibitors of cyclin dependent kinases that were able to form a new interaction with an identified residue of the protein, Lys89. Compounds from this series have shown no detectable effect when tested against a representative set of other serine/threonine kinases such as GSK3beta, CAMKII, PKA, PKC-alpha,beta,epsilon,gamma. Compound 2i inhibits proliferation in HCT 116 cells in tissue culture. Synthesis, co-crystal structure of CDK2 in complex with compound 2i, and preliminary SAR study are disclosed.

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Organizational Affiliation: 
• Lilly Research Laboratories, A Division of Eli Lilly and Company, Lilly Corporate Center, DC: 0540, Indianapolis, IN 46285, United States. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.44 kDa 
• Atom Count: 2,530 
• Modeled 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 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 GTEx:  ENSG00000123374

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
628	B [auth A]	4-{[6-(2,6-DICHLOROBENZOYL)IMIDAZO[1,2-A]PYRIDIN-2-YL]AMINO}BENZENESULFONAMIDE C20 H14 Cl2 N4 O3 S UQAWGIKJINAKIZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
628	BindingDB:  1YKR	IC50: 560 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.271 (Depositor) 
• R-Value Work:  0.255 (Depositor) 
• R-Value Observed: 0.260 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.25	α = 90
b = 71.393	β = 90
c = 71.418	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-24 
Deposition Author(s): Hamdouchi, C., Zhong, B., Mendoza, J., Jaramillo, C., Zhang, F., Brooks, H.B.

Revision History  

• Version 1.0: 2006-01-24
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description