2R64 | pdb_00002r64

Crystal structure of a 3-aminoindazole compound with CDK2

PDB DOI: https://doi.org/10.2210/pdb2R64/pdb

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

Deposited: 2007-09-05 Released: 2008-09-09
Deposition Author(s): Lee, J., Choi, H., Kim, K.H., Jeong, S., Park, J.W., Baek, C.S., Lee, S.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.257 (Depositor), 0.251 (DCC)
R-Value Work:
0.221 (Depositor), 0.217 (DCC)
R-Value Observed:
0.221 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Synthesis and biological evaluation of 3,5-diaminoindazoles as cyclin-dependent kinase inhibitors.

Lee, J., Choi, H., Kim, K.H., Jeong, S., Park, J.W., Baek, C.S., Lee, S.H.

(2008) Bioorg Med Chem Lett 18: 2292-2295

PubMed: 18353638 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2008.03.002
Primary Citation Related Structures:
2R64

PubMed Abstract:
A novel series of 3,5-diaminoindazoles were prepared and found to be CDK inhibitors. Potent inhibitors against CDK1 and CDK2 were obtained by introduction of 1lambda(6)-isothiazolidine-1,1-dioxide at 5-position of indazole. Anti-proliferative activities of compounds were evaluated using EJ, HCT116, SW620, and A549 cancer cell lines.

Organizational Affiliation

Department of Chemistry, Keimyung University, 1000 Sindang-Dong, Dalseo-Gu, Daegu 704-701, South Korea. jinho@kmu.ac.kr

Macromolecule Content

Total Structure Weight: 34.43 kDa
Atom Count: 2,349
Modeled Residue Count: 279
Deposited Residue Count: 298
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division protein kinase 2	A	298	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P24941
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
740 Query on 740 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	N-[5-(1,1-DIOXIDOISOTHIAZOLIDIN-2-YL)-1H-INDAZOL-3-YL]-2-(4-PIPERIDIN-1-YLPHENYL)ACETAMIDE C₂₃ H₂₇ N₅ O₃ S ZXYIRNXOAJYLCU-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.257 (Depositor), 0.251 (DCC)
R-Value Work: 0.221 (Depositor), 0.217 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.449	α = 90
b = 71.279	β = 90
c = 71.985	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-09-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-09-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-03-13
Changes: Data collection, Database references, Derived calculations