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- PDB-6ahs: Mouse Kallikrein 7 in complex with imidazolinylindole derivative -

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Basic information

Entry
Database: PDB / ID: 6ahs
TitleMouse Kallikrein 7 in complex with imidazolinylindole derivative
ComponentsKallikrein-7
KeywordsHYDROLASE / protease
Function / homology
Function and homology information


stratum corneum chymotryptic enzyme / positive regulation of antibacterial peptide production / epidermal lamellar body / Degradation of the extracellular matrix / cornified envelope / serine-type endopeptidase activity / proteolysis / extracellular space
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-9YO / Kallikrein-7
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSugawara, H.
Citation
Journal: Bioorg. Med. Chem. Lett. / Year: 2019
Title: Discovery and structure-activity relationship of imidazolinylindole derivatives as kallikrein 7 inhibitors.
Authors: Murafuji, H. / Muto, T. / Goto, M. / Imajo, S. / Sugawara, H. / Oyama, Y. / Minamitsuji, Y. / Miyazaki, S. / Murai, K. / Fujioka, H.
#1: Journal: Bioorg. Med. Chem. Lett. / Year: 2017
Title: Discovery and structure-activity relationship study of 1,3,6-trisubstituted 1,4-diazepane-7-ones as novel human kallikrein 7 inhibitors.
Authors: Murafuji, H. / Sakai, H. / Goto, M. / Imajo, S. / Sugawara, H. / Muto, T.
#2: Journal: Bioorg. Med. Chem. Lett. / Year: 2018
Title: Structure-based drug design of 1,3,6-trisubstituted 1,4-diazepan-7-ones as selective human kallikrein 7 inhibitors.
Authors: Murafuji, H. / Sakai, H. / Goto, M. / Oyama, Y. / Imajo, S. / Sugawara, H. / Tomoo, T. / Muto, T.
#3: Journal: Bioorg. Med. Chem. / Year: 2018
Title: Structure-based drug design to overcome species differences in kallikrein 7 inhibition of 1,3,6-trisubstituted 1,4-diazepan-7-ones.
Authors: Murafuji, H. / Sugawara, H. / Goto, M. / Oyama, Y. / Sakai, H. / Imajo, S. / Tomoo, T. / Muto, T.
History
DepositionAug 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2185
Polymers24,6371
Non-polymers5814
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area10600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.156, 71.156, 98.907
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

21A-526-

HOH

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Components

#1: Protein Kallikrein-7 / Serine protease 6 / Stratum corneum chymotryptic enzyme / Thymopsin


Mass: 24637.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Klk7, Prss6, Scce / Production host: Escherichia coli (E. coli)
References: UniProt: Q91VE3, stratum corneum chymotryptic enzyme
#2: Chemical ChemComp-9YO / 1-[(2-chlorophenyl)sulfonyl]-5-methyl-3-[(4R)-2-methyl-4,5-dihydro-1H-imidazol-4-yl]-1H-indole


Mass: 387.883 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18ClN3O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 8000, PEG 400, magnesium chloride, Tris/HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→100 Å / Num. obs: 26249 / % possible obs: 99.1 % / Redundancy: 13.2 % / Net I/σ(I): 17.6
Reflection shellResolution: 1.75→1.78 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZFH

5zfh


Resolution: 1.75→30.29 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.055 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.023 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21177 1279 5 %RANDOM
Rwork0.16729 ---
obs0.16943 24117 96.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.665 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2--0.61 Å20 Å2
3----1.23 Å2
Refinement stepCycle: 1 / Resolution: 1.75→30.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1716 0 36 142 1894
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191797
X-RAY DIFFRACTIONr_bond_other_d0.0010.021641
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.9812441
X-RAY DIFFRACTIONr_angle_other_deg0.70233844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.855223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.46825.07765
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68515312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.538155
X-RAY DIFFRACTIONr_chiral_restr0.1110.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.0211942
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02325
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7421.76896
X-RAY DIFFRACTIONr_mcbond_other1.7191.755894
X-RAY DIFFRACTIONr_mcangle_it2.2622.6251117
X-RAY DIFFRACTIONr_mcangle_other2.2652.6271118
X-RAY DIFFRACTIONr_scbond_it3.1462.203901
X-RAY DIFFRACTIONr_scbond_other3.1272.202901
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6693.1651325
X-RAY DIFFRACTIONr_long_range_B_refined6.4122.7882013
X-RAY DIFFRACTIONr_long_range_B_other6.40222.4731996
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.747→1.793 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 70 -
Rwork0.24 1263 -
obs--69.21 %
Refinement TLS params.Method: refined / Origin x: -18.5818 Å / Origin y: 26.1766 Å / Origin z: 43.6988 Å
111213212223313233
T0.1335 Å2-0.0103 Å20.0109 Å2-0.1232 Å2-0.0163 Å2--0.0045 Å2
L0.458 °2-0.0869 °2-0.1459 °2-1.0834 °20.1368 °2--0.4958 °2
S0.0081 Å °-0.0407 Å °0.0015 Å °0.0432 Å °-0.0352 Å °0.0339 Å °0.0217 Å °-0.0097 Å °0.0271 Å °

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