8I0M | pdb_00008i0m

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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free: 
  0.282 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Structure of CDK6 in complex with inhibitor

Jiang, C., Ye, Y., Huang, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.56 kDa 
• Atom Count: 2,080 
• Modeled Residue Count: 260 
• Deposited Residue Count: 301 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NJ6 (Subject of Investigation/LOI)	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free:  0.282 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

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

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-24 
Deposition Author(s): Jiang, C., Ye, Y., Huang, Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

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