3S2P

Crystal structure of CDK2 with a 2-aminopyrimidine compound

PDB DOI: https://doi.org/10.2210/pdb3S2P/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2011-05-17 Released: 2011-07-20
Deposition Author(s): Kim, K.-H., Lee, J., Jeong, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.304
R-Value Work: 0.246
R-Value Observed: 0.246

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Discovery of a novel class of 2-aminopyrimidines as CDK1 and CDK2 inhibitors

Lee, J., Kim, K.-H., Jeong, S.

(2011) Bioorg Med Chem Lett 21: 4203-4205

PubMed: 21684737 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2011.05.081
Primary Citation of Related Structures:
3S2P

PubMed Abstract:
A series of new 2-(2-aminopyrimidin-4-yl)phenol derivatives were synthesized as potential antitumor compounds. Substitution with pyrrolidine-3,4-diol at the 4-position of phenol provided potent inhibitory activity against CDK1 and CDK2. X-ray crystal structural studies were performed to account for the effect of the substituent on both the enzymatic and cell growth inhibitory activities.

Organizational Affiliation

Department of Chemistry, Keimyung University, Daegu 704-701, South Korea. jinho@kmu.ac.kr

Macromolecule Content

Total Structure Weight: 34.31 kDa
Atom Count: 2,311
Modelled Residue Count: 279
Deposited Residue Count: 298
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	298	Homo sapiens	Mutation(s): 0 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
PMU Query on PMU 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]	(3S,4S)-1-{3-[2-amino-6-(propan-2-yl)pyrimidin-4-yl]-4-hydroxyphenyl}pyrrolidine-3,4-diol C₁₇ H₂₂ N₄ O₃ VIUGBRHEHAGOFV-HOTGVXAUSA-N		Interactions Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
PMU	PDBBind: 3S2P	IC50: 68 (nM) from 1 assay(s)
PMU	BindingDB: 3S2P	IC50: 68 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.304
R-Value Work: 0.246
R-Value Observed: 0.246
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.777	α = 90
b = 71.058	β = 90
c = 72.123	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-07-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-07-20
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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.