4A4X

NEK2-EDE bound to CCT248662

PDB DOI: https://doi.org/10.2210/pdb4A4X/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2011-10-20 Released: 2012-04-25
Deposition Author(s): Mas-Droux, C., Bayliss, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.247
R-Value Work: 0.204
R-Value Observed: 0.206

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Design of Potent and Selective Hybrid Inhibitors of the Mitotic Kinase Nek2: Structure-Activity Relationship, Structural Biology, and Cellular Activity.

Innocenti, P., Cheung, K.M., Solanki, S., Mas-Droux, C., Rowan, F., Yeoh, S., Boxall, K., Westlake, M., Pickard, L., Hardy, T., Baxter, J.E., Aherne, G.W., Bayliss, R., Fry, A.M., Hoelder, S.

(2012) J Med Chem 55: 3228

PubMed: 22404346 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/jm201683b
Primary Citation of Related Structures:
4A4X, 4AFE

PubMed Abstract:
We report herein a series of Nek2 inhibitors based on an aminopyridine scaffold. These compounds have been designed by combining key elements of two previously discovered chemical series. Structure based design led to aminopyridine (R)-21, a potent and selective inhibitor able to modulate Nek2 activity in cells.

Organizational Affiliation

Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, United Kingdom.

Macromolecule Content

Total Structure Weight: 33.29 kDa
Atom Count: 2,172
Modelled Residue Count: 253
Deposited Residue Count: 279
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN KINASE NEK2	A	279	Homo sapiens	Mutation(s): 3 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P51955 (Homo sapiens) Explore P51955 Go to UniProtKB: P51955
PHAROS: P51955 GTEx: ENSG00000117650
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P51955
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JUP Query on JUP 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]	4-(2-AMINO-5-{4-[(DIMETHYLAMINO)METHYL]THIOPHEN-2-YL}PYRIDIN-3-YL)-2-{(1R)-1-[2-(TRIFLUOROMETHYL)PHENYL]ETHOXY}BENZAMIDE C₂₈ H₂₇ F₃ N₄ O₂ S DNZGEPPZYMAFLN-MRXNPFEDSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
JUP	BindingDB: 4A4X	IC50: min: 37, max: 2700 (nM) from 3 assay(s)
JUP	PDBBind: 4A4X	IC50: 59 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.247
R-Value Work: 0.204
R-Value Observed: 0.206
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.223	α = 90
b = 56.909	β = 127.12
c = 74.408	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-04-25

Deposition Author(s):

Mas-Droux, C.

Bayliss, R.

Revision History (Full details and data files)

Version 1.0: 2012-04-25
Type: Initial release
Version 1.1: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other