2C4G | pdb_00002c4g

STRUCTURE OF CDK2-CYCLIN A WITH PHA-533514

PDB DOI: https://doi.org/10.2210/pdb2C4G/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Trichoplusia ni, Escherichia coli BL21
Mutation(s): No

Deposited: 2005-10-19 Released: 2005-11-23
Deposition Author(s): Cameron, A., Fogliatto, G., Pevarello, P., Fancelli, D., Vulpetti, A., Amici, R., Villa, M., Pittala, V., Ciomei, M., Mercurio, C., Bischoff, J.R., Roletto, F., Varasi, M., Brasca, M.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.250 (Depositor), 0.224 (DCC)
R-Value Work:
0.233 (Depositor), 0.226 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

3-Amino-1,4,5,6-Tetrahydropyrrolo[3,4-C]Pyrazoles: A New Class of Cdk2 Inhibitors.

Pevarello, P., Fancelli, D., Vulpetti, A., Amici, R., Villa, M., Pittala, V., Vianello, P., Cameron, A., Ciomei, M., Mercurio, C., Bischoff, J.R., Roletto, F., Varasi, M., Brasca, M.G.

(2006) Bioorg Med Chem Lett 16: 1084

PubMed: 16290148 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2005.10.071
Primary Citation Related Structures:
2C4G

PubMed Abstract:
We have recently reported about a new class of Aurora-A inhibitors based on a bicyclic tetrahydropyrrolo[3,4-c]pyrazole scaffold. Here we describe the synthesis and early expansion of CDK2/cyclin A-E inhibitors belonging to the same chemical class. Synthesis of the compounds was accomplished using a solution-phase protocol amenable to rapid parallel expansion. Compounds with nanomolar activity in the biochemical assay and able to efficiently inhibit CDK2-mediated tumor cell proliferation have been obtained.

Organizational Affiliation

Department of Chemistry, Nerviano Medical Science, BU-Oncology, Via Pasteur 10, 20014 Nerviano MI, Italy. paolo.pevarello@nervianoms.com

Macromolecule Content

Total Structure Weight: 131.79 kDa
Atom Count: 9,187
Modeled Residue Count: 1,117
Deposited Residue Count: 1,148
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CELL DIVISION PROTEIN KINASE 2	A, C	309	Homo sapiens	Mutation(s): 0 EC: 2.7.1.37 (PDB Primary Data), 2.7.11.22 (UniProt)
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P24941
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLIN A2	B, D	265	Homo sapiens	Mutation(s): 0
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20248
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
514 Query on 514 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth C]	F [auth A], G [auth C]	(3Z)-5-ACETYL-3-(BENZOYLIMINO)-3,6-DIHYDROPYRROLO[3,4-C]PYRAZOL-5-IUM C₁₄ H₁₁ N₄ O₂ SWJVFMCHEFMLDD-FYWRMAATSA-N		Interactions Focus chain F [auth A] Focus chain G [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth D]	E [auth A], H [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.250 (Depositor), 0.224 (DCC)
R-Value Work: 0.233 (Depositor), 0.226 (DCC)

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 191.985	α = 90
b = 191.985	β = 90
c = 205.88	γ = 120

Software Package:

Software Name	Purpose
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2005-11-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-11-23
Type: Initial release
Version 1.1: 2011-05-07
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: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description