Macromolecule Content

Total Structure Weight: 34.55 kDa
Atom Count: 2550
Modelled Residue Count: 283
Deposited Residue Count: 299
Unique protein chains: 1

4FKV

Crystal structure of the cdk2 in complex with oxindole inhibitor

DOI: 10.2210/pdb4FKV/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2012-06-13 Released: 2013-05-08
Deposition Author(s): Kang, Y.N., Stuckey, J.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.203
R-Value Work: 0.176
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of the cdk2 in 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
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 2	A	299	Homo sapiens	Mutation(s): 1 Gene Names: CDK2, CDKN2 EC: 2.7.11.22
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens) Explore P24941 Go to UniProtKB: P24941
PHAROS: P24941 GTEx: ENSG00000123374
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
61K Query on 61K Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	(3Z)-N-[2-(1H-imidazol-4-yl)ethyl]-2-oxo-3-[2-(4-sulfamoylphenyl)hydrazinylidene]-2,3-dihydro-1H-indole-5-carboxamide C₂₀ H₁₉ N₇ O₄ S CQSUILWVYSOEJC-UHFFFAOYSA-N		Ligand Interaction
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
61K	ΔG: 39 kJ/mol BindingDB
61K	-TΔS: 6.289999961853027 kJ/mol BindingDB
61K	Kd: 82.19999694824219 nM BindingDB
61K	ΔH: 18 kJ/mol BindingDB
61K	Kd: 251 nM BindingDB
61K	ΔH: 44.79999923706055 kJ/mol BindingDB
61K	ΔG: 40.400001525878906 kJ/mol BindingDB
61K	-TΔS: 22.350000381469727 kJ/mol BindingDB

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.203
R-Value Work: 0.176
R-Value Observed: 0.177
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.657	α = 90
b = 71.914	β = 90
c = 72.096	γ = 90

Software Package:

Software Name	Purpose
MD2	data collection
PHASER	phasing
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2012-06-13
Released Date: 2013-05-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-05-08
Type: Initial release
Version 1.1: 2013-05-22
Changes: Other

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.