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- PDB-4a9s: CRYSTAL STRUCTURE OF HUMAN CHK2 IN COMPLEX WITH BENZIMIDAZOLE CAR... -

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Basic information

Entry
Database: PDB / ID: 4a9s
TitleCRYSTAL STRUCTURE OF HUMAN CHK2 IN COMPLEX WITH BENZIMIDAZOLE CARBOXAMIDE INHIBITOR
ComponentsSERINE/THREONINE-PROTEIN KINASE CHK2
KeywordsTRANSFERASE
Function / homology
Function and homology information


mitotic DNA damage checkpoint signaling / regulation of autophagosome assembly / mitotic intra-S DNA damage checkpoint signaling / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / thymocyte apoptotic process / regulation of protein catabolic process / replicative senescence / mitotic spindle assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / signal transduction in response to DNA damage ...mitotic DNA damage checkpoint signaling / regulation of autophagosome assembly / mitotic intra-S DNA damage checkpoint signaling / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / thymocyte apoptotic process / regulation of protein catabolic process / replicative senescence / mitotic spindle assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / signal transduction in response to DNA damage / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / regulation of signal transduction by p53 class mediator / DNA damage checkpoint signaling / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Stabilization of p53 / protein catabolic process / G2/M DNA damage checkpoint / PML body / Regulation of TP53 Activity through Methylation / cellular response to gamma radiation / intrinsic apoptotic signaling pathway in response to DNA damage / G2/M transition of mitotic cell cycle / Regulation of TP53 Degradation / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Regulation of TP53 Activity through Phosphorylation / protein autophosphorylation / non-specific serine/threonine protein kinase / protein stabilization / protein phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / ubiquitin protein ligase binding / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / protein homodimerization activity / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site ...Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Chem-RU9 / Serine/threonine-protein kinase Chk2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsMatijssen, C. / Silva-Santisteban, M.C. / Westwood, I.M. / Siddique, S. / Choi, V. / Sheldrake, P. / van Montfort, R.L.M. / Blagg, J.
CitationJournal: Bioorg.Med.Chem. / Year: 2012
Title: Benzimidazole Inhibitors of the Protein Kinase Chk2: Clarification of the Binding Mode by Flexible Side Chain Docking and Protein-Ligand Crystallography.
Authors: Matijssen, C. / Silva-Santisteban, M.C. / Westwood, I.M. / Siddique, S. / Choi, V. / Sheldrake, P. / Van Montfort, R.L.M. / Blagg, J.
History
DepositionNov 28, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Nov 7, 2012Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN KINASE CHK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5193
Polymers37,1121
Non-polymers4072
Water50428
1
A: SERINE/THREONINE-PROTEIN KINASE CHK2
hetero molecules

A: SERINE/THREONINE-PROTEIN KINASE CHK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0386
Polymers74,2242
Non-polymers8154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area2680 Å2
ΔGint-14.5 kcal/mol
Surface area28030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.710, 90.710, 93.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE CHK2 / CHK2 CHECKPOINT HOMOLOG / CDS1 HOMOLOG / HUCDS1 / HCDS1 / CHECKPOINT KINASE 2


Mass: 37111.844 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 210-531
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: HUMAN CDNA LIBRARY / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 PLYSS
References: UniProt: O96017, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-RU9 / 2-(4-(3-HYDROXYPHENOXY)PHENYL)-1H-BENZO[D]IMIDAZOLE-5-CARBOXAMIDE


Mass: 345.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H15N3O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details2-(4-(3-HYDROXYPHENOXY)PHENYL)-1H-BENZO[D]IMIDAZOLE-5-CARBOXAMIDE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.7 % / Description: NONE
Crystal growDetails: 0.1M HEPES PH 7.5, 0.2M MAGNESIUM NITRATE, 8-16% (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.66→78.56 Å / Num. obs: 12863 / % possible obs: 98.4 % / Observed criterion σ(I): 1.5 / Redundancy: 3.4 % / Biso Wilson estimate: 69.41 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.5
Reflection shellResolution: 2.66→2.8 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.2 / % possible all: 93.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WTJ

2wtj


Resolution: 2.66→40.104 Å / SU ML: 0.77 / σ(F): 1.36 / Phase error: 21.25 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2335 641 5 %
Rwork0.1863 --
obs0.1885 12852 97.93 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.197 Å2 / ksol: 0.292 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.9839 Å20 Å20 Å2
2---0.9839 Å20 Å2
3---1.9677 Å2
Refinement stepCycle: LAST / Resolution: 2.66→40.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 30 28 2256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042303
X-RAY DIFFRACTIONf_angle_d0.7413126
X-RAY DIFFRACTIONf_dihedral_angle_d18.004840
X-RAY DIFFRACTIONf_chiral_restr0.05360
X-RAY DIFFRACTIONf_plane_restr0.003389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6602-2.86560.33021350.2952317X-RAY DIFFRACTION95
2.8656-3.15380.25451320.23742435X-RAY DIFFRACTION100
3.1538-3.60990.26171150.1872484X-RAY DIFFRACTION100
3.6099-4.54710.18991340.16032468X-RAY DIFFRACTION99
4.5471-40.10890.23581250.17732507X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.0171-2.8908-1.13242.47480.59082.0427-0.8972-0.91120.10410.79120.6658-0.08130.15540.39640.1860.68160.1977-0.06990.4532-0.10450.516238.2384-42.37211.7741
24.4383-2.5413-0.33654.84070.6722.317-0.2299-0.23230.1197-0.3124-0.0716-0.49830.46280.52680.21170.43790.0478-0.01060.3150.01890.278728.1941-31.37298.2738
31.6248-0.879-1.18471.00690.6125.31720.1318-0.00920.5323-0.31230.036-0.0228-0.31520.0932-0.07640.25860.0581-0.04390.19270.00870.438717.2925-17.447717.1956
41.98410.13460.85031.2012-0.26360.42670.01830.3628-0.4288-0.788-0.37930.55510.1675-0.27070.21230.6635-0.0456-0.11710.4153-0.00250.294316.1912-31.1842-0.238
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 211:287)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 288:379)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 380:466)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 467:512)

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