Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34437.81 
• Atom Count: 2428 
• Residue Count: 298 
• Unique protein chains: 1

1YKR

Crystal structure of cdk2 with an aminoimidazo pyridine inhibitor

• DOI: 10.2210/pdb1YKR/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus


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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.271 
• R-Value Work: 0.255 

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: 10.1016/j.bmcl.2005.01.052


• 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.

---

Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cell division protein kinase 2	A	298	Homo sapiens	Mutation(s): 0  Gene Names: CDK2 (CDKN2) EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens) Go to Gene View: CDK2 Go to UniProtKB:  P24941

Small Molecules

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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
628	IC50: 560 nM BINDINGMOAD
628	IC50: 560 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.271 
• R-Value Work: 0.255 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 53.250	α = 90.00
b = 71.393	β = 90.00
c = 71.418	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-01-18 
• 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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance