2VTH

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

Structural Biology Knowledgebase: 2VTH SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.198

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2VTH

Classification: TRANSFERASE

Total Structure Weight: 34292.15

Macromolecule Entities
Molecule Chains Length Organism Details
CELL DIVISION PROTEIN KINASE 2 A 298 Homo sapiens EC#: 2.7.11.22 IUBMB
Gene Name(s): CDK2 Gene View CDKN2

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
LZ2
Query on LZ2

A 5-hydroxynaphthalene-1-sulfonamide
C10 H9 N O3 S
NFVBVKHGDDDCEA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
LZ2 N/A in BindingDB
IC50: 120000 nM  BindingMOAD
IC50: 120000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.198
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 53.48 α = 90.00
b = 71.65 β = 90.00
c = 72.18 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



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

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4