8I0M

Structure of CDK6 in complex with inhibitor

PDB DOI: https://doi.org/10.2210/pdb8I0M/pdb

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

Deposited: 2023-01-11 Released: 2024-01-24
Deposition Author(s): Jiang, C., Ye, Y., Huang, Y.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.78 Å
R-Value Free: 0.282
R-Value Work: 0.203
R-Value Observed: 0.207

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of CDK6 in complex with inhibitor

Jiang, C., Ye, Y., Huang, Y.

To be published.

Macromolecule Content

Total Structure Weight: 34.56 kDa
Atom Count: 2,080
Modelled Residue Count: 260
Deposited Residue Count: 301
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 6	A	301	Homo sapiens	Mutation(s): 0 Gene Names: CDK6, CDKN6 EC: 2.7.11.22
UniProt & NIH Common Fund Data Resources
Find proteins for Q00534 (Homo sapiens) Explore Q00534 Go to UniProtKB: Q00534
PHAROS: Q00534 GTEx: ENSG00000105810
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q00534
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NJ6 (Subject of Investigation/LOI) Query on NJ6 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]	2-[(4-azanylcyclohexyl)amino]-7-cyclopentyl-~{N},~{N}-dimethyl-pyrrolo[2,3-d]pyrimidine-6-carboxamide C₂₀ H₃₀ N₆ O HZJPJDOVXYTUTI-SHTZXODSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.78 Å
R-Value Free: 0.282
R-Value Work: 0.203
R-Value Observed: 0.207
Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.87	α = 90
b = 100.87	β = 90
c = 59.48	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-01-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-01-24
Type: Initial release

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.