2C6T | pdb_00002c6t

Crystal structure of the human CDK2 complexed with the triazolopyrimidine inhibitor

PDB DOI: https://doi.org/10.2210/pdb2C6T/pdb

Classification: CELL CYCLE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2005-11-11 Released: 2005-12-07
Deposition Author(s): Richardson, C.M., Dokurno, P., Murray, J.B., Surgenor, A.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free:
0.257 (Depositor)
R-Value Work:
0.200 (Depositor)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Triazolo[1,5-A]Pyrimidines as Novel Cdk2 Inhibitors: Protein Structure-Guided Design and Sar.

Richardson, C.M., Williamson, D.S., Parratt, M.J., Borgognoni, J., Cansfield, A.D., Dokurno, P., Francis, G.L., Howes, R., Moore, J.D., Murray, J.B., Robertson, A., Surgenor, A.E., Torrance, C.J.

(2006) Bioorg Med Chem Lett 16: 1353

PubMed: 16325401 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2005.11.048
Primary Citation Related Structures:
2C68, 2C69, 2C6I, 2C6K, 2C6L, 2C6M, 2C6O, 2C6T

PubMed Abstract:
Crystallographic and modelling data, in conjunction with a medicinal chemistry template-hopping approach, led to the identification of a series of novel and potent inhibitors of human cyclin-dependent kinase 2 (CDK2), with selectivity over glycogen synthase kinase-3beta (GSK-3beta). One example had a CDK2 IC(50) of 120 nM and showed selectivity over GSK-3beta of 167-fold.

Organizational Affiliation

Vernalis (R&D) Ltd, Granta Park, Great Abington, Cambridge CB1 6GB, UK.

Macromolecule Content

Total Structure Weight: 128.14 kDa
Atom Count: 9,341
Modeled Residue Count: 1,108
Deposited Residue Count: 1,112
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	298	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	258	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DT5 Query on DT5 Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain E [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth A]	E [auth A], F [auth C]	4-{[5-(CYCLOHEXYLOXY)[1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-YL]AMINO}BENZENESULFONAMIDE C₁₇ H₂₀ N₆ O₃ S RPJIMTALCNCQLV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth C]

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

Binding Affinity Annotations
ID	Source	Binding Affinity
DT5	BindingDB: 2C6T	IC50: 350 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free: 0.257 (Depositor)
R-Value Work: 0.200 (Depositor)
R-Value Observed: 0.202 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.418	α = 90
b = 161.345	β = 90
c = 66.221	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2005-12-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-12-07
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: 2019-03-06
Changes: Data collection, Derived calculations, Experimental preparation, Other
Version 1.4: 2019-04-03
Changes: Data collection, Experimental preparation
Version 1.5: 2023-12-13
Changes: Data collection, Database references, Other, Refinement description
Version 1.6: 2024-10-23
Changes: Structure summary