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 
  • R-Value Observed: 0.192 

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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-dependent kinase 2A, C298Homo sapiensMutation(s): 0 
Gene Names: CDK2CDKN2
EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
NIH Common Fund Data Resources
PHAROS:  P24941
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-A2B, D258Homo sapiensMutation(s): 0 
Gene Names: CCN1CCNACCNA2Cyclin A
Find proteins for P20248 (Homo sapiens)
Explore P20248 
Go to UniProtKB:  P20248
NIH Common Fund Data Resources
PHAROS:  P20248
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
60K
Query on 60K

Download Ideal Coordinates CCD File 
E [auth A], H [auth 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 Ideal Coordinates CCD File 
F [auth A], G [auth B], I [auth D]2,3-DIHYDROXY-1,4-DITHIOBUTANE
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
60KKd:  8   nM  BindingDB
60KΔH:  62.7599983215332   kJ/mol  BindingDB
60KΔH:  14.199999809265137   kJ/mol  BindingDB
60K-TΔS:  19.459999084472656   kJ/mol  BindingDB
60K-TΔS:  24.31999969482422   kJ/mol  BindingDB
60KKd:  179   nM  BindingDB
60KΔG:  40.400001525878906   kJ/mol  BindingDB
60KΔG:  37.099998474121094   kJ/mol  BindingDB
60KΔH:  38.400001525878906   kJ/mol  BindingDB
60KKd:  99   nM  BindingDB
60KKd:  419   nM  BindingDB
60KΔH:  18   kJ/mol  BindingDB
60KKd:  98.5999984741211   nM  BindingDB
60K-TΔS:  1.340000033378601   kJ/mol  BindingDB
60KΔG:  38.29999923706055   kJ/mol  BindingDB
60KKd:  334   nM  BindingDB
60KΔG:  39   kJ/mol  BindingDB
60K-TΔS:  6.289999961853027   kJ/mol  BindingDB
60K-TΔS:  22.350000381469727   kJ/mol  BindingDB
60KKd:  8.430000305175781   nM  BindingDB
60KΔH:  44.79999923706055   kJ/mol  BindingDB
60KΔG:  33.70000076293945   kJ/mol  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.661α = 90
b = 163.623β = 106.78
c = 72.609γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
MD2data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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