4EK6

Crystal structure of the cdk2 in complex with aminopyrazole inhibitor

PDB DOI: https://doi.org/10.2210/pdb4EK6/pdb

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

Deposited: 2012-04-09 Released: 2013-05-01
Deposition Author(s): Kang, Y.N., Stuckey, J.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.52 Å
R-Value Free: 0.217
R-Value Work: 0.188
R-Value Observed: 0.189

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the cdk2 in complex with aminopyrazole inhibitor

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

To be published.

Macromolecule Content

Total Structure Weight: 34.33 kDa
Atom Count: 2,614
Modelled Residue Count: 279
Deposited Residue Count: 299
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P24941
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
10K Query on 10K Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	N-(3-cyclopropyl-1H-pyrazol-5-yl)-2-[4-(thiophen-2-yl)phenyl]acetamide C₁₈ H₁₇ N₃ O S LQBKAYJFACGUCC-UHFFFAOYSA-N		Interactions Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
10K	BindingDB: 4EK6	Kd: min: 79, max: 4960 (nM) from 3 assay(s)
10K	BindingDB: 4EK6	IC50: 3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.52 Å
R-Value Free: 0.217
R-Value Work: 0.188
R-Value Observed: 0.189
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.328	α = 90
b = 71.647	β = 90
c = 72.332	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-05-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-05-01
Type: Initial release
Version 1.1: 2013-05-08
Changes: Database references
Version 1.2: 2013-05-29
Changes: Other
Version 1.3: 2017-11-15
Changes: Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.