4BZD | pdb_00004bzd

Structure of CDK2 in complex with a benzimidazopyrimidine

• PDB DOI: https://doi.org/10.2210/pdb4BZD/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2013-07-25 Released: 2014-08-13 
• Deposition Author(s): Tucker, J.A., Valentine, A., Stanway, J., Brassington, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.204 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: other

Literature

Structure of Cdk2 in Complex with a Benzimidazopyrimidine

Rye, C.

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: 34.45 kDa 
• Atom Count: 2,472 
• Modeled Residue Count: 277 
• Deposited Residue Count: 299 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLIN-DEPENDENT KINASE 2	A	299	Homo sapiens	Mutation(s): 0  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
D6I	C [auth A]	6-(benzimidazol-1-yl)-N-[5-[3-(dimethylamino)propoxy]pyridin-2-yl]pyrimidin-4-amine C21 H23 N7 O VKUXBRRQHBTQPW-UHFFFAOYSA-N
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.204 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.456	α = 90
b = 71.884	β = 90
c = 72.291	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-13 
Deposition Author(s): Tucker, J.A., Valentine, A., Stanway, J., Brassington, C.

Revision History  

• Version 1.0: 2014-08-13
  Type: Initial release
  
• Version 1.1: 2018-04-04
  Changes: Data collection
• Version 1.2: 2019-04-24
  Changes: Data collection, Source and taxonomy
• Version 1.3: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary