Download MendeleyCDK2/cyclin A2 in complex with open-ring 5-nitrosopyrimidine inhibitor LC436
Skerlova, J., Rezacova, P., Brynda, J.To be published.
6RIJ
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
- Funding Organization(s): Ministry of Education (Czech Republic)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.238
- R-Value Work: 0.203
- R-Value Observed: 0.205
This is version 1.1 of the entry. See complete history.
Literature
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 | 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 Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P24941 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cyclin-A2 | 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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P20248 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| K4W (Subject of Investigation/LOI) Query on K4W | 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 Query on GOL | H [auth B], I [auth B], L [auth C], N [auth D] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| NA Query on 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 Query on 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
- R-Value Work: 0.203
- R-Value Observed: 0.205
- 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 Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| MOLREP | phasing |
| PDB_EXTRACT | data extraction |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-07-22 Deposition Author(s): Skerlova, J., Rezacova, P., Brynda, J.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Ministry of Education (Czech Republic) | Czech Republic | programme NPU I: LO1304 |
Revision History (Full details and data files)
- 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
