3SW7

Crystal Structure of the CDK2 in complex with thiazolylpyrimidine inhibitor

PDB DOI: https://doi.org/10.2210/pdb3SW7/pdb

Classification: transferase/transferase inhibitor
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2011-07-13 Released: 2012-08-01
Deposition Author(s): Kang, Y.N., Stuckey, J.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.215
R-Value Work: 0.183
R-Value Observed: 0.184

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of the CDK2 in complex with thiazolylpyrimidine inhibitor

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

To be published.

Macromolecule Content

Total Structure Weight: 34.37 kDa
Atom Count: 2,419
Modelled Residue Count: 279
Deposited Residue Count: 299
Unique protein chains: 1

Macromolecules

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(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 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
19K Query on 19K Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	N~4~-[4-(2,4-dimethyl-1,3-thiazol-5-yl)pyrimidin-2-yl]-N~1~,N~1~-dimethyl-2-nitrobenzene-1,4-diamine C₁₇ H₁₈ N₆ O₂ S MYHBMTAGTIOCHM-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
19K	BindingDB: 3SW7	Kd: min: 61.7, max: 5804 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.215
R-Value Work: 0.183
R-Value Observed: 0.184
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.638	α = 90
b = 72.041	β = 90
c = 72.419	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-08-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-08-01
Type: Initial release
Version 1.1: 2013-05-29
Changes: Other
Version 1.2: 2017-11-08
Changes: Refinement description

RCSB PDB Core Operations are 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.