Macromolecule Content

Total Structure Weight: 34.54 kDa
Atom Count: 2261
Modelled Residue Count: 278
Deposited Residue Count: 303
Unique protein chains: 1

5OO1

Cdk2(F80C, C177A) covalent adduct with C37 at F80C

PDB DOI: 10.2210/pdb5OO1/pdb

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

Deposited: 2017-08-04 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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.236
R-Value Work: 0.185
R-Value Observed: 0.187

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P24941
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9Z2 (Subject of Investigation/LOI) Query on 9Z2 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	~{N}-(4-pyrimidin-2-ylphenyl)propanamide C₁₃ H₁₃ N₃ O AYWSBVNLDJWGBC-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.236
R-Value Work: 0.185
R-Value Observed: 0.187
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.576	α = 90
b = 66.486	β = 90
c = 70.053	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Deposited Date: 2017-08-04
Released Date: 2018-08-29

Deposition Author(s):

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 (Full details and data files)

Version 1.0: 2018-08-29
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.