Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 34292.82 
• Atom Count: 2276 
• Residue Count: 298 
• Unique protein chains: 1

2VTI

Identification of N-(4-piperidinyl)-4-(2,6-dichlorobenzoylamino)-1H- pyrazole-3-carboxamide (AT7519), a Novel Cyclin Dependent Kinase Inhibitor Using Fragment-Based X-Ray Crystallography and Structure Based Drug Design.

• DOI: 10.2210/pdb2VTI/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda


• Deposited: 2008-05-15 Released: 2008-08-05 
• Deposition Author(s): Wyatt, P.G., Woodhead, A.J., Boulstridge, J.A., Berdini, V., Carr, M.G., Cross, D.M., Danillon, D., Davis, D.J., Devine, L.A., Early, T.R., Feltell, R.E., Lewis, E.J., McMenamin, R.L., Navarro, E.F., O'Brien, M.A., O'Reilly, M., Reule, M., Saxty, G., Seavers, L.C.A., Smith, D., Squires, M.S., Trewartha, G., Walker, M.T., Woolford, A.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.199 
• R-Value Work: 0.167 

Literature

Identification of N-(4-Piperidinyl)-4-(2,6-Dichlorobenzoylamino)-1H-Pyrazole-3-Carboxamide (at7519), a Novel Cyclin Dependent Kinase Inhibitor Using Fragment-Based X-Ray Crystallography and Structure Based Drug Design.

Wyatt, P.G., Woodhead, A.J., Berdini, V., Boulstridge, J.A., Carr, M.G., Cross, D.M., Davis, D.J., Devine, L.A., Early, T.R., Feltell, R.E., Lewis, E.J., Mcmenamin, R.L., Navarro, E.F., O'Brien, M.A., O'Reilly, M., Reule, M., Saxty, G., Seavers, L.C.A., Smith, D., Squires, M.S., Trewartha, G., Walker, M.T., Woolford, A.J.

(2008) J.Med.Chem. 51: 4986

• PubMed: 18656911 
• DOI: 10.1021/jm800382h
• Primary Citation of Related Structures:  
  2VTT, 2VTS, 2VTR, 2VTP, 2VTO, 2VTN, 2VTL, 2VTJ, 2VU3, 2VTQ, 2VTM, 2VTH, 2VTA
• Also Cited By: 5FP5, 5FP6


• PubMed Abstract: 
  

The application of fragment-based screening techniques to cyclin dependent kinase 2 (CDK2) identified multiple (>30) efficient, synthetically tractable small molecule hits for further optimization. Structure-based design approaches led to the identification of multiple lead series, which retained the key interactions of the initial binding fragments and additionally explored other areas of the ATP binding site. The majority of this paper details the structure-guided optimization of indazole (6) using information gained from multiple ligand-CDK2 cocrystal structures. Identification of key binding features for this class of compounds resulted in a series of molecules with low nM affinity for CDK2. Optimisation of cellular activity and characterization of pharmacokinetic properties led to the identification of 33 (AT7519), which is currently being evaluated in clinical trials for the treatment of human cancers.

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Organizational Affiliation: 

Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom. [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
LZ3	A	N-(4-sulfamoylphenyl)-1H-indazole-3-carboxamide C14 H12 N4 O3 S MNHPHKFLWAPNOV-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
LZ3	IC50: 660 nM (100) BINDINGDB
LZ3	IC50: 660 nM BINDINGMOAD
LZ3	IC50: 660 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.199 
• R-Value Work: 0.167 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 53.097	α = 90.00
b = 71.770	β = 90.00
c = 71.894	γ = 90.00

Software Package:

Software Name	Purpose
CrystalClear	data reduction
BUSTER-TNT	refinement
AMoRE	phasing
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-05-15 
• Released Date: 2008-08-05 
• Deposition Author(s): Wyatt, P.G., Woodhead, A.J., Boulstridge, J.A., Berdini, V., Carr, M.G., Cross, D.M., Danillon, D., Davis, D.J., Devine, L.A., Early, T.R., Feltell, R.E., Lewis, E.J., McMenamin, R.L., Navarro, E.F., O'Brien, M.A., O'Reilly, M., Reule, M., Saxty, G., Seavers, L.C.A., Smith, D., Squires, M.S., Trewartha, G., Walker, M.T., Woolford, A.J.

Revision History 

• Version 1.0: 2008-08-05
  Type: Initial release
• Version 1.1: 2011-05-08
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-07-12
  Type: Data collection