1OGU | pdb_00001ogu

STRUCTURE OF HUMAN THR160-PHOSPHO CDK2/CYCLIN A COMPLEXED WITH A 2-ARYLAMINO-4-CYCLOHEXYLMETHYL-5-NITROSO-6-AMINOPYRIMIDINE INHIBITOR

PDB DOI: https://doi.org/10.2210/pdb1OGU/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2003-05-13 Released: 2003-09-02
Deposition Author(s): Pratt, D.J., Endicott, J.A., Noble, M.E.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.260 (Depositor), 0.254 (DCC)
R-Value Work:
0.198 (Depositor), 0.194 (DCC)
R-Value Observed:
0.201 (Depositor)

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

Structure-Based Design of 2-Arylamino-4-Cyclohexyl Methyl-5-Nitroso-6-Aminopyrimidine Inhibitors of Cyclin-Dependent Kinases 1 and 2

Sayle, K.L., Bentley, J., Boyle, F.T., Calvert, A.H., Cheng, Y., Curtin, N.J., Endicott, J.A., Golding, B.T., Hardcastle, I.R., Jewsbury, P., Mesguiche, V., Newell, D.R., Noble, M.E.M., Parsons, R.J., Pratt, D.J., Wang, L.Z., Griffin, R.J.

(2003) Bioorg Med Chem Lett 13: 3079

PubMed: 12941338 Search on PubMed
DOI: https://doi.org/10.1016/s0960-894x(03)00651-6
Primary Citation Related Structures:
1OGU

PubMed Abstract:
A series of O(4)-cyclohexylmethyl-5-nitroso-6-aminopyrimidines bearing 2-arylamino substituents was synthesised and evaluated for CDK1 and CDK2 inhibitory activity. Consistent with analogous studies with O(6)-cyclohexylmethylpurines, 2-arylaminopyrimidines with a sulfonamide or carboxamide group at the 4'-position were potent inhibitors, with IC(50) values against CDK2 of 1.1+/-0.3 and 34+/-8 nM, respectively. The crystal structure of the 4'-carboxamide derivative, in complex with phospho-Thr160 CDK2/cyclin A, confirmed the expected binding mode of the inhibitor, and revealed an additional interaction between the carboxamide function and an aspartate residue.

Organizational Affiliation

Northern Institute for Cancer Research, School of Natural Sciences-Chemistry, Bedson Building, University of Newcastle, Newcastle Upon Tyne NE1 7RU, UK.

Macromolecule Content

Total Structure Weight: 129.44 kDa
Atom Count: 8,893
Modeled Residue Count: 1,078
Deposited Residue Count: 1,124
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	302	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	260	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
ST8 Query on ST8 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth C] mmCIF format, chain E [auth A] mmCIF format, chain G [auth C]	E [auth A], G [auth C]	4-{[4-AMINO-6-(CYCLOHEXYLMETHOXY)-5-NITROSOPYRIMIDIN-2-YL]AMINO}BENZAMIDE C₁₈ H₂₂ N₆ O₃ YBKLJTXDSBEVRV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth C]
SGM Query on SGM Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain H [auth D] MOL2 format, chain F [auth B] MOL2 format, chain H [auth D] mmCIF format, chain F [auth B] mmCIF format, chain H [auth D]	F [auth B], H [auth D]	MONOTHIOGLYCEROL C₃ H₈ O₂ S PJUIMOJAAPLTRJ-GSVOUGTGSA-N		Interactions Focus chain F [auth B] Focus chain H [auth D] Interactions & Density Focus chain F [auth B] Focus chain H [auth D]

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
ST8	BindingDB: 1OGU	IC50: 34 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.260 (Depositor), 0.254 (DCC)
R-Value Work: 0.198 (Depositor), 0.194 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.836	α = 90
b = 133.676	β = 90
c = 148.335	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2003-09-02

Deposition Author(s):

Pratt, D.J.

Endicott, J.A.

Noble, M.E.M.

Revision History (Full details and data files)

Version 1.0: 2003-09-02
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: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.4: 2024-11-06
Changes: Structure summary