- FASTA Sequence
- PDBx/mmCIF Format
- PDBx/mmCIF Format (gz)
- BinaryCIF Format (gz)
- Legacy PDB Format
- Legacy PDB Format (gz)
- PDBML/XML Format (gz)
- Structure Factors (CIF)
- Structure Factors (CIF - gz)
- Validation Full (PDF - gz)
- Validation (XML - gz)
- Validation (CIF - gz)
- Validation 2fo-fc coefficients (CIF - gz)
- Validation fo-fc coefficients (CIF - gz)
- Biological Assembly 1 (CIF - gz)
- Biological Assembly 2 (CIF - gz)
- Biological Assembly 1 (PDB - gz)
- Biological Assembly 2 (PDB - gz)
1VYW | pdb_00001vyw
Structure of CDK2/Cyclin A with PNU-292137
- PDB DOI: https://doi.org/10.2210/pdb1VYW/pdb
- Classification: TRANSFERASE
- Organism(s): Homo sapiens
- Expression System: Spodoptera frugiperda, Escherichia coli BL21
- Mutation(s): No
- Deposited: 2004-05-07 Released: 2004-06-10
- Deposition Author(s): Pevarello, P., Brasca, M.G., Amici, R., Orsini, P., Traquandi, G., Corti, L., Piutti, C., Sansonna, P., Villa, M., Pierce, B.S., Pulici, M., Giordano, P., Martina, K., Fritzen, E.L., Nugent, R.A., Casale, E., Cameron, A., Ciomei, M., Roletto, F., Isacchi, A., Fogliatto, G., Pesenti, E., Pastori, W., Marsiglio, A., Leach, K.L., Clare, P.M., Fiorentini, F., Varasi, M., Vulpetti, A., Warpehoski, M.A.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.258 (Depositor), 0.220 (DCC)
- R-Value Work: 0.229 (Depositor), 0.230 (DCC)
- 👁 Image
Download Mendeley
3-Aminopyrazole Inhibitors of Cdk2/Cyclin a as Antitumor Agents. Part 1. Lead Finding
Pevarello, P., Brasca, M.G., Amici, R., Orsini, P., Traquandi, G., Corti, L., Piutti, C., Sansonna, P., Villa, M., Pierce, B.S., Pulici, M., Giordano, P., Martina, K., Fritzen, E.L., Nugent, R.A., Casale, E., Cameron, A., Ciomei, M., Roletto, F., Isacchi, A., Fogliatto, G., Pesenti, E., Pastori, W., Marsiglio, A., Leach, K.L., Clare, P.M., Fiorentini, F., Varasi, M., Vulpetti, A., Warpehoski, M.A.(2004) J Med Chem 47: 3367
- PubMed: 15189033 Search on PubMed
- DOI: https://doi.org/10.1021/jm031145u
- Primary Citation Related Structures:
1VYW, 1VYZ - PubMed Abstract:
Abnormal proliferation mediated by disruption of the normal cell cycle mechanisms is a hallmark of virtually all cancer cells. Compounds targeting complexes between cyclin-dependent kinases (CDK) and cyclins, such as CDK2/cyclin A and CDK2/cyclin E, and inhibiting their kinase activity are regarded as promising antitumor agents to complement the existing therapies. From a high-throughput screening effort, we identified a new class of CDK2/cyclin A/E inhibitors. The hit-to-lead expansion of this class is described. X-ray crystallographic data of early compounds in this series, as well as in vitro testing funneled for rapidly achieving in vivo efficacy, led to a nanomolar inhibitor of CDK2/cyclin A (N-(5-cyclopropyl-1H-pyrazol-3-yl)-2-(2-naphthyl)acetamide (41), PNU-292137, IC50 = 37 nM) with in vivo antitumor activity (TGI > 50%) in a mouse xenograft model at a dose devoid of toxic effects.
- Chemistry Department, Pharmacia Italia, Viale Pasteur 10, 20014 Nerviano (MI), Italy. paolo.pevarello@pharmacia.com
Organizational Affiliation:
Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (292)
Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (292)
Global Symmetry: Asymmetric - C1
Global Stoichiometry: Hetero 2-mer - A1B1
Find Similar Assemblies
Biological assembly 1 assigned by authors and generated by PISA (software)
Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (292)
Global Symmetry: Asymmetric - C1
Global Stoichiometry: Hetero 2-mer - A1B1
Find Similar Assemblies
Biological assembly 2 assigned by authors and generated by PISA (software)
Macromolecule Content
- Total Structure Weight: 131.84 kDa
- Atom Count: 9,442
- Modeled Residue Count: 1,114
- Deposited Residue Count: 1,148
- Unique protein chains: 2
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| CELL DIVISION PROTEIN KINASE 2 | 309 | Homo sapiens | Mutation(s): 0 EC: 2.7.1.37 (PDB Primary Data), 2.7.11.22 (UniProt) | 👁 Image | |
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 | |||||
| |||||
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| CYCLIN A2 | 265 | Homo sapiens | Mutation(s): 0 | 👁 Image | |
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 | |||||
| |||||
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 292 Query on 292 Download Ideal Coordinates CCD File | F [auth A], G [auth C] | N-(3-CYCLOPROPYL-1H-PYRAZOL-5-YL)-2-(2-NAPHTHYL)ACETAMIDE C18 H17 N3 O RIGZCVNCFXYBEG-UHFFFAOYSA-N | 👁 Image | ||
| SO4 Query on SO4 Download Ideal Coordinates CCD File | E [auth A], H [auth D] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | 👁 Image | ||
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.258 (Depositor), 0.220 (DCC)
- R-Value Work: 0.229 (Depositor), 0.230 (DCC)
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 184.223 | α = 90 |
| b = 184.223 | β = 90 |
| c = 214.72 | γ = 120 |
| Software Name | Purpose |
|---|---|
| CNX | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| CNX | phasing |
Deposition Data
- Released Date: 2004-06-10 Deposition Author(s): Pevarello, P., Brasca, M.G., Amici, R., Orsini, P., Traquandi, G., Corti, L., Piutti, C., Sansonna, P., Villa, M., Pierce, B.S., Pulici, M., Giordano, P., Martina, K., Fritzen, E.L., Nugent, R.A., Casale, E., Cameron, A., Ciomei, M., Roletto, F., Isacchi, A., Fogliatto, G., Pesenti, E., Pastori, W., Marsiglio, A., Leach, K.L., Clare, P.M., Fiorentini, F., Varasi, M., Vulpetti, A., Warpehoski, M.A.
Revision History (Full details and data files)
- Version 1.0: 2004-06-10
Type: Initial release - Version 1.1: 2011-05-08
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 1.3: 2019-04-03
Changes: Data collection, Other, Source and taxonomy - Version 1.4: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other
