6RIJ | pdb_00006rij

CDK2/cyclin A2 in complex with open-ring 5-nitrosopyrimidine inhibitor LC436

• PDB DOI: https://doi.org/10.2210/pdb6RIJ/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-04-24 Released: 2020-07-22 
• Deposition Author(s): Skerlova, J., Rezacova, P., Brynda, J.
• Funding Organization(s): Ministry of Education (Czech Republic)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.238 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

CDK2/cyclin A2 in complex with open-ring 5-nitrosopyrimidine inhibitor LC436

Skerlova, J., Rezacova, P., Brynda, J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 128.74 kDa 
• Atom Count: 9,097 
• Modeled Residue Count: 1,092 
• Deposited Residue Count: 1,114 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 2	A, C	299	Homo sapiens	Mutation(s): 0  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-A2	B, D	258	Homo sapiens	Mutation(s): 0  Gene Names: CCNA2, CCN1, CCNA
UniProt & NIH Common Fund Data Resources
Find proteins for P20248 (Homo sapiens) Explore P20248  Go to UniProtKB:  P20248
PHAROS:  P20248 GTEx:  ENSG00000145386

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K4W (Subject of Investigation/LOI)	E [auth A], J [auth C]	4-[[[5-nitroso-2-[[(2~{R})-1-oxidanylbutan-2-yl]amino]-6-(propan-2-ylamino)pyrimidin-4-yl]amino]methyl]phenol C18 H26 N6 O3 JREKZOMBYITGOF-CYBMUJFWSA-N
GOL	H [auth B], I [auth B], L [auth C], N [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	F [auth A], G [auth B], K [auth C], M [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.238 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.31	α = 90
b = 148.06	β = 90.51
c = 162.96	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-22 
Deposition Author(s): Skerlova, J., Rezacova, P., Brynda, J.

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Funding Organization	Location	Grant Number
Ministry of Education (Czech Republic)	Czech Republic	programme NPU I: LO1304

Revision History  

• Version 1.0: 2020-07-22
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary