7SJ3

Structure of CDK4-Cyclin D3 bound to abemaciclib

• PDB DOI: https://doi.org/10.2210/pdb7SJ3/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2021-10-15 Released: 2022-11-02 
• Deposition Author(s): Hilgers, M.T., Pelletier, L.A.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 
  0.234 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Models: experimental

Literature

Structure of CDK4-Cyclin D3 bound to abemaciclib

Hilgers, M.T., Pelletier, L.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 64.56 kDa 
• Atom Count: 4,100 
• Modelled Residue Count: 517 
• Deposited Residue Count: 570 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 4	A	311	Homo sapiens	Mutation(s): 1  Gene Names: CDK4 EC: 2.7.11.22
UniProt & NIH Common Fund Data Resources
Find proteins for P11802 (Homo sapiens) Explore P11802  Go to UniProtKB:  P11802
PHAROS:  P11802 GTEx:  ENSG00000135446

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
G1/S-specific cyclin-D3	B	259	Homo sapiens	Mutation(s): 0  Gene Names: CCND3
UniProt & NIH Common Fund Data Resources
Find proteins for P30281 (Homo sapiens) Explore P30281  Go to UniProtKB:  P30281
PHAROS:  P30281 GTEx:  ENSG00000112576

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6ZV (Subject of Investigation/LOI)	C [auth A]	N-{5-[(4-ethylpiperazin-1-yl)methyl]pyridin-2-yl}-5-fluoro-4-[4-fluoro-2-methyl-1-(propan-2-yl)-1H-benzimidazol-6-yl]py rimidin-2-amine C27 H32 F2 N8 UZWDCWONPYILKI-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Binding Affinity Annotations
ID	Source	Binding Affinity
6ZV	BindingDB:  7SJ3	Ki: min: 2, max: 8.2 (nM) from 2 assay(s)
		IC50: min: 0.26, max: 1700 (nM) from 18 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.234 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.654	α = 90
b = 117.654	β = 90
c = 170.278	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-02 
Deposition Author(s): Hilgers, M.T., Pelletier, L.A.

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Funding Organization	Location	Grant Number
Other private	United States	NA

Revision History  

• Version 1.0: 2022-11-02
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary