2VTT

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.

• PDB DOI:  https://doi.org/10.2210/pdb2VTT/pdb

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


• 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: 1.68 Å
• R-Value Free: 0.227 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

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: 4986-4999

• PubMed: 18656911 
• DOI: https://doi.org/10.1021/jm800382h
• Primary Citation of Related Structures:  
  2VTA, 2VTH, 2VTI, 2VTJ, 2VTL, 2VTM, 2VTN, 2VTO, 2VTP, 2VTQ, 2VTR, 2VTS, 2VTT, 2VU3


• 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]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 34.33 kDa 
• Atom Count: 2,438 
• Modelled Residue Count: 272 
• 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: 2.7.11.1 (PDB Primary Data), 2.7.11.22 (PDB Primary Data)
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
LZD	B [auth A]	4-{[(2,6-difluorophenyl)carbonyl]amino}-N-[(3S)-piperidin-3-yl]-1H-pyrazole-3-carboxamide C16 H17 F2 N5 O2 KOMNQBZWMCFDTQ-VIFPVBQESA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
LZD	BindingDB:  2VTT	IC50: 44 (nM) from 1 assay(s)
	PDBBind:  2VTT	IC50: 44 (nM) from 1 assay(s)
	Binding MOAD:  2VTT	IC50: 44 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.227 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.567	α = 90
b = 71.476	β = 90
c = 72.116	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-06-20
  Changes: Data collection, Database references