3U9N | pdb_00003u9n

X-ray crystal structure of compound 1 bound to human CHK1 kinase domain

PDB DOI: https://doi.org/10.2210/pdb3U9N/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2011-10-19 Released: 2012-01-25
Deposition Author(s): Fischmann, T.O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.229 (Depositor), 0.242 (DCC)
R-Value Work:
0.196 (Depositor), 0.211 (DCC)
R-Value Observed:
0.197 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3U9N

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Discovery of a Novel Series of CHK1 Kinase Inhibitors with Distinctive Hinge Binding Mode

Huang, X., Cheng, C.C., Fischmann, T.O., Duca, J.S., Yang, X., Richards, M., Shipps Jr., G.W.

(2012) ACS Med Chem Lett

Macromolecule Content

Total Structure Weight: 31.86 kDa
Atom Count: 2,291
Modeled Residue Count: 258
Deposited Residue Count: 273
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase Chk1	A	273	Homo sapiens	Mutation(s): 0 Gene Names: CHEK1, CHK1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O14757 (Homo sapiens) Explore O14757 Go to UniProtKB: O14757
PHAROS: O14757 GTEx: ENSG00000149554
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O14757
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
09H Query on 09H 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]	2-(2,3-dihydro-1-benzofuran-5-yl)-N-[2-(piperazin-1-yl)phenyl]-1,3-thiazole-4-carboxamide C₂₂ H₂₂ N₄ O₂ S WRGSHXQBWJUKQD-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
09H	BindingDB: 3U9N	Kd: 100 (nM) from 1 assay(s)
		IC50: 75 (nM) from 1 assay(s)
		EC50: 1.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.229 (Depositor), 0.242 (DCC)
R-Value Work: 0.196 (Depositor), 0.211 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.16	α = 90
b = 65.68	β = 102.63
c = 54.78	γ = 90

Software Package:

Software Name	Purpose
JDirector	data collection
TNT	refinement
BUSTER	refinement
DENZO	data reduction
SCALEPACK	data scaling
TNT	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-01-25

Deposition Author(s):

Fischmann, T.O.

Revision History (Full details and data files)

Version 1.0: 2012-01-25
Type: Initial release
Version 1.1: 2012-02-01
Changes: Database references
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.