5OO3 | pdb_00005oo3

Cdk2(F80C, C177A) with covalent ligand at F80C

• PDB DOI: https://doi.org/10.2210/pdb5OO3/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-08-05 Released: 2018-08-29 
• Deposition Author(s): Craven, G., Morgan, R.M.L., Mann, D.J.
• Funding Organization(s): Engineering and Physical Sciences Research Council, Cancer and Polio Research Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

High-throughput kinetic analysis for target-directed covalent ligand discovery

Craven, G., Affron, D.P., Allen, C.E., Greener, J.G., Morgan, R.M.L., Matthies, S., Armstrong, A., Mann, D.J.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 34.53 kDa 
• Atom Count: 2,585 
• Modeled Residue Count: 286 
• Deposited Residue Count: 303 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 2	A	303	Homo sapiens	Mutation(s): 2  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9ZB (Subject of Investigation/LOI)	B [auth A]	1-(4-ethyl-2,3-dihydroquinoxalin-1-yl)propan-1-one C13 H18 N2 O VDEKFYBSRAMPIS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.11	α = 90
b = 70.97	β = 90
c = 72.43	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-08-29 
Deposition Author(s): Craven, G., Morgan, R.M.L., Mann, D.J.

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Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	EP/F500416/1
Cancer and Polio Research Fund	United Kingdom	--

Revision History  

• Version 1.0: 2018-08-29
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary