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- PDB-2cgv: Identification of chemically diverse Chk1 inhibitors by receptor-... -

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Basic information

Entry
Database: PDB / ID: 2cgv
TitleIdentification of chemically diverse Chk1 inhibitors by receptor- based virtual screening
ComponentsSERINE/THREONINE-PROTEIN KINASE CHK1
KeywordsTRANSFERASE / DOCKING / DRUG DESIGN / ONCOLOGY / VIRTUAL SCREENING / ATP- BINDING / CELL CYCLE / DNA DAMAGE / DNA REPAIR / KINASE / NUCLEAR PROTEIN / NUCLEOTIDE-BINDING / PHOSPHORYLATION / POLYMORPHISM / SERINE/THREONINE-PROTEIN KINASE / UBL CONJUGATION
Function / homology
Function and homology information


regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage / histone kinase activity (H3-T11 specific) / negative regulation of mitotic nuclear division / regulation of histone H3-K9 acetylation / chromatin-mediated maintenance of transcription / regulation of mitotic centrosome separation / signal transduction involved in G2 DNA damage checkpoint / regulation of double-strand break repair via homologous recombination / DNA damage induced protein phosphorylation / negative regulation of G0 to G1 transition ...regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage / histone kinase activity (H3-T11 specific) / negative regulation of mitotic nuclear division / regulation of histone H3-K9 acetylation / chromatin-mediated maintenance of transcription / regulation of mitotic centrosome separation / signal transduction involved in G2 DNA damage checkpoint / regulation of double-strand break repair via homologous recombination / DNA damage induced protein phosphorylation / negative regulation of G0 to G1 transition / replicative senescence / positive regulation of cell cycle / condensed nuclear chromosome / DNA damage checkpoint / chromatin / cellular response to mechanical stimulus / peptidyl-threonine phosphorylation / kinase activity / regulation of signal transduction by p53 class mediator / DNA replication / non-specific serine/threonine protein kinase / intracellular signal transduction / cell cycle / protein kinase activity / centrosome / DNA repair / intracellular membrane-bounded organelle / protein domain specific binding / cellular response to DNA damage stimulus / apoptotic process / protein serine/threonine kinase activity / protein phosphorylation / protein-containing complex / extracellular space / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Serine/threonine-protein kinase, active site / Protein kinase domain / Protein kinase domain / Checkpoint kinase 1, catalytic domain / Protein kinase, ATP binding site / Protein kinase-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...Serine/threonine-protein kinase, active site / Protein kinase domain / Protein kinase domain / Checkpoint kinase 1, catalytic domain / Protein kinase, ATP binding site / Protein kinase-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Serine/threonine-protein kinase Chk1
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFoloppe, N. / Fisher, L.M. / Howes, R. / Potter, A. / Robertson, A.G.S. / Surgenor, A.E.
CitationJournal: Bioorg.Med.Chem. / Year: 2006
Title: Identification of Chemically Diverse Chk1 Inhibitors by Receptor-Based Virtual Screening.
Authors: Foloppe, N. / Fisher, L.M. / Howes, R. / Potter, A. / Robertson, A.G.S. / Surgenor, A.E.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 9, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN KINASE CHK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4102
Polymers34,1481
Non-polymers2621
Water2,900161
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)44.945, 65.681, 54.867
Angle α, β, γ (deg.)90.00, 102.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE CHK1 / CHK1 KINASE


Mass: 34148.148 Da / Num. of mol.: 1 / Fragment: N-TERMINAL KINASE DOMAIN, RESIDUES 1-289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC1/CHK1 1-289 C8H / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O14757, EC: 2.7.1.37
#2: Chemical ChemComp-3B3 / (2S)-1-AMINO-3-[(5-NITROQUINOLIN-8-YL)AMINO]PROPAN-2-OL


Mass: 262.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14N4O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Compound detailsREQUIRED FOR CHECKPOINT MEDIATED CELL CYCLE ARREST IN RESPONSE TO DNA DAMAGE OR THE PRESENCE OF ...REQUIRED FOR CHECKPOINT MEDIATED CELL CYCLE ARREST IN RESPONSE TO DNA DAMAGE OR THE PRESENCE OF UNREPLICATED DNA

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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: 2.9 Å3/Da / Density % sol: 56.9 %
Crystal growpH: 7.5 / Details: pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 10278 / % possible obs: 79.9 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.2
Reflection shellResolution: 2.6→2.66 Å / Redundancy: 0.8 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.2 / % possible all: 36

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Processing

Software
NameVersionClassification
REFMAC5.1.09refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IA8

1ia8


Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.872 / SU B: 12.006 / SU ML: 0.252 / Cross valid method: THROUGHOUT / ESU R Free: 0.397 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 379 4.7 %RANDOM
Rwork0.179 ---
Obs0.183 7633 82.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.47 Å2
Baniso -1Baniso -2Baniso -3
1--3.47 Å20 Å20.04 Å2
2---0.47 Å20 Å2
3---3.96 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2134 0 19 161 2314
Refine LS restraints
Refinement-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0212204
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.7281.972984
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5495262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.76715391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4661514
X-RAY DIFFRACTIONr_chiral_restr0.1730.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021672
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2590.21051
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2142
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.330.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined1.3410.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.461.51317
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.67122129
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8883887
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.0274.5855
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.299 11
Rwork0.228 280

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