2WTD | pdb_00002wtd

Crystal structure of Chk2 in complex with an inhibitor

PDB DOI: https://doi.org/10.2210/pdb2WTD/pdb

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

Deposited: 2009-09-15 Released: 2009-12-29
Deposition Author(s): Hilton, S., Naud, S., Caldwell, J.J., Boxall, K., Burns, S., Anderson, V.E., Antoni, L., Allen, C.E., Pearl, L.H., Oliver, A.W., Aherne, G.W., Garrett, M.D., Collins, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.258 (Depositor), 0.258 (DCC)
R-Value Work:
0.191 (Depositor), 0.189 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Identification and Characterisation of 2-Aminopyridine Inhibitors of Checkpoint Kinase 2

Hilton, S., Naud, S., Caldwell, J.J., Boxall, K., Burns, S., Anderson, V.E., Antoni, L., Allen, C.E., Pearl, L.H., Oliver, A.W., Aherne, G.W., Garrett, M.D., Collins, I.

(2010) Bioorg Med Chem 18: 707

PubMed: 20022510 Search on PubMed
DOI: https://doi.org/10.1016/j.bmc.2009.11.058
Primary Citation Related Structures:
2WTC, 2WTD, 2WTI, 2WTJ

PubMed Abstract:
5-(Hetero)aryl-3-(4-carboxamidophenyl)-2-aminopyridine inhibitors of CHK2 were identified from high throughput screening of a kinase-focussed compound library. Rapid exploration of the hits through straightforward chemistry established structure-activity relationships and a proposed ATP-competitive binding mode which was verified by X-ray crystallography of several analogues bound to CHK2. Variation of the 5-(hetero)aryl substituent identified bicyclic dioxolane and dioxane groups which improved the affinity and the selectivity of the compounds for CHK2 versus CHK1. The 3-(4-carboxamidophenyl) substituent could be successfully replaced by acyclic omega-aminoalkylamides, which made additional polar interactions within the binding site and led to more potent inhibitors of CHK2. Compounds from this series showed activity in cell-based mechanistic assays for inhibition of CHK2.

Organizational Affiliation

Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK.

Macromolecule Content

Total Structure Weight: 37.69 kDa
Atom Count: 2,357
Modeled Residue Count: 285
Deposited Residue Count: 329
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN KINASE CHK2	A	329	Homo sapiens	Mutation(s): 0 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O96017 (Homo sapiens) Explore O96017 Go to UniProtKB: O96017
PHAROS: O96017 GTEx: ENSG00000183765
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O96017
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZZK Query on ZZK 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-(1,3-BENZODIOXOL-4-YL)PYRIDIN-3-YL]BENZAMIDE C₁₉ H₁₅ N₃ O₃ UBOGEBHIZSQBBD-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.258 (Depositor), 0.258 (DCC)
R-Value Work: 0.191 (Depositor), 0.189 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.89	α = 90
b = 90.89	β = 90
c = 92.83	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-12-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-12-29
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: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description