4FX3

Crystal Structure of the CDK2/Cyclin A complex with oxindole inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of the CDK2/Cyclin A complex with oxindole inhibitor

Kang, Y.N.Stuckey, J.A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 2
A, C
298Homo sapiensMutation(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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cyclin-A2
B, D
258Homo sapiensMutation(s): 0 
Gene Names: CCNA2 (CCN1, CCNA)
Find proteins for P20248 (Homo sapiens)
Go to Gene View: CCNA2
Go to UniProtKB:  P20248
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
60K
Query on 60K

Download SDF File 
Download CCD File 
A, C
(3Z)-2-oxo-3-[2-(4-sulfamoylphenyl)hydrazinylidene]-2,3-dihydro-1H-indole-5-carboxylic acid
C15 H12 N4 O5 S
JHTDQQNFBRWRSP-UHFFFAOYSA-N
 Ligand Interaction
DTT
Query on DTT

Download SDF File 
Download CCD File 
A, B, D
2,3-DIHYDROXY-1,4-DITHIOBUTANE
1,4-DITHIOTHREITOL
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
60KKd: 99 - 419 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 70.661α = 90.00
b = 163.623β = 106.78
c = 72.609γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
BUSTERrefinement
HKL-2000data scaling
BUSTER-TNTrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
DENZOdata reduction
MD2data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-15
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description