3EOC | pdb_00003eoc

Cdk2/CyclinA complexed with a imidazo triazin-2-amine

PDB DOI: https://doi.org/10.2210/pdb3EOC/pdb

Classification: TRANSFERASE/CELL CYCLE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda, Escherichia coli
Mutation(s): No

Deposited: 2008-09-26 Released: 2008-11-04
Deposition Author(s): Cheung, M., Kuntz, K., Pobanz, M., Salovich, J., Wilson, B., Andrews, W., Shewchuk, L., Epperly, A., Hassler, D., Leesnitzer, M., Smith, J., Smith, G., Lansing, T., Mook, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.238 (Depositor), 0.238 (DCC)
R-Value Work:
0.215 (Depositor), 0.213 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Imidazo[5,1-f][1,2,4]triazin-2-amines as novel inhibitors of polo-like kinase 1.

Cheung, M., Kuntz, K.W., Pobanz, M., Salovich, J.M., Wilson, B.J., Andrews, C.W., Shewchuk, L.M., Epperly, A.H., Hassler, D.F., Leesnitzer, M.A., Smith, J.L., Smith, G.K., Lansing, T.J., Mook, R.A.

(2008) Bioorg Med Chem Lett 18: 6214-6217

PubMed: 18929484 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2008.09.100
Primary Citation Related Structures:
3EOC

PubMed Abstract:
The synthesis and biological activities of imidazo[5,1-f][1,2,4]triazin-2-amines (imidazotriazines) as novel polo-like kinase 1 inhibitors are reported.

Organizational Affiliation

GlaxoSmithKline, Fire Moore Drive, Research Triangle Park, NC 27709, USA. mui.h.cheung@gsk.com

Macromolecule Content

Total Structure Weight: 128.47 kDa
Atom Count: 8,772
Modeled Residue Count: 1,102
Deposited Residue Count: 1,116
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 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 Gene Names: CDK2 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

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-A2	B, D	260	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% 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
T2A Query on T2A 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]	5-methyl-7-phenyl-N-(3,4,5-trimethoxyphenyl)imidazo[5,1-f][1,2,4]triazin-2-amine C₂₁ H₂₁ N₅ O₃ HOOQLZPFGONGJY-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]

Binding Affinity Annotations
ID	Source	Binding Affinity
T2A	BindingDB: 3EOC	IC50: 230 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.238 (Depositor), 0.238 (DCC)
R-Value Work: 0.215 (Depositor), 0.213 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.977	α = 90
b = 182.977	β = 90
c = 213.687	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
DENZO	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-11-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-11-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Refinement description
Version 1.4: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description