8YNG | pdb_00008yng

CDK2 and compounds and inhibors

PDB DOI: https://doi.org/10.2210/pdb8YNG/pdb

Classification: CELL CYCLE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-11 Released: 2025-03-19
Deposition Author(s): Ge, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free:
0.235 (Depositor), 0.239 (DCC)
R-Value Work:
0.190 (Depositor), 0.196 (DCC)
R-Value Observed:
0.194 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 8YNG

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

CDK2 and compounds and inhibors

Ge, S.

To be published.

Macromolecule Content

Total Structure Weight: 34.67 kDa
Atom Count: 2,563
Modeled Residue Count: 295
Deposited Residue Count: 301
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 2	A	301	Homo sapiens	Mutation(s): 0 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P24941
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1D6S (Subject of Investigation/LOI) Query on A1D6S 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]	8-(1-methylpiperidin-4-yl)-2-[(1-methylsulfonylpiperidin-4-yl)amino]-7-oxidanylidene-pyrido[2,3-d]pyrimidine-6-carbonitrile C₂₀ H₂₇ N₇ O₃ S XHOIOLGPJDOFQU-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.235 (Depositor), 0.239 (DCC)
R-Value Work: 0.190 (Depositor), 0.196 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.55	α = 90
b = 71.28	β = 90
c = 71.77	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-03-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-03-19
Type: Initial release

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.