3QRT

CDK2 in complex with inhibitor NSK-MC2-55

• PDB DOI: https://doi.org/10.2210/pdb3QRT/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-02-18 Released: 2012-08-08 
• Deposition Author(s): Betzi, S., Alam, R., Han, H., Becker, A., Schonbrunn, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.221 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 

Starting Model: experimental

Literature

Structure-guided optimization of novel CDK2 inhibitors discovered by high-throughput screening

Schonbrunn, E., Becker, A., Betzi, S., Alam, R., Han, H., Rawle, F., Katta, V., Jakkaraj, J., Chakrasali, R., Neelam, S., Hook, D., Tash, J., Georg, G.

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)

Macromolecule Content

• Total Structure Weight: 35.29 kDa 
• Atom Count: 2,627 
• Modelled Residue Count: 294 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 2	A	306	Homo sapiens	Mutation(s): 0  Gene Names: CDK2 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X14	D [auth A]	(5R)-5-(2-methylbutan-2-yl)-N-(4-sulfamoylbenzyl)-4,5,6,7-tetrahydro-2H-indazole-3-carboxamide C20 H28 N4 O3 S CPRLKIUEXBBIHS-CQSZACIVSA-N
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.221 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.68	α = 90
b = 71.77	β = 90
c = 72.6	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
CNS	refinement
XDS	data reduction
XDS	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-08 
Deposition Author(s): Betzi, S., Alam, R., Han, H., Becker, A., Schonbrunn, E.

Revision History  

• Version 1.0: 2012-08-08
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description