1VYW

STRUCTURE OF CDK2/CYCLIN A WITH PNU-292137

Structural Biology Knowledgebase: 1VYW SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.229

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1VYW

Classification: TRANSFERASE

Total Structure Weight: 131837.62

Macromolecule Entities
Molecule Chains Length Organism Details
CELL DIVISION PROTEIN KINASE 2 A, C 309 Homo sapiens EC#: 2.7.11.22 IUBMB
Gene Name(s): CDK2 Gene View CDKN2
CYCLIN A2 B, D 265 Homo sapiens Fragment: C-TERMINAL PORTION, RESIDUES 174-432
Gene Name(s): CCNA2 Gene View CCN1 CCNA

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
292
Query on 292

A, C N-(3-CYCLOPROPYL-1H-PYRAZOL-5-YL)-2-(2-NAPHTHYL)ACETAMIDE
PNU-292137 INHIBITOR (Synonym)
C18 H17 N3 O
RIGZCVNCFXYBEG-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, D SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
292 IC50: 37 nM (100) BindingDB

IC50: 37 nM  BindingMOAD
IC50: 37 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.229
  • Space Group: P 62 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 184.22 α = 90.00
b = 184.22 β = 90.00
c = 214.72 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-05-07
  • Released Date: 2004-06-10
  • Deposition author(s): Pevarello, P., Brasca, M.G., Amici, R., Orsini, P., Traquandi, G., Corti, L., Piutti, C., Sansonna, P., Villa, M., Pierce, B.S., Pulici, M., Giordano, P., Martina, K., Fritzen, E.L., Nugent, R.A., Casale, E., Cameron, A., Ciomei, M., Roletto, F., Isacchi, A., Fogliatto, G., Pesenti, E., Pastori, W., Marsiglio, A., Leach, K.L., Clare, P.M., Fiorentini, F., Varasi, M., Vulpetti, A., Warpehoski, M.A.

Revision History

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