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- PDB-3s0n: Crystal Structure of Human Chymase with Benzimidazolone Inhibitor -

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Basic information

Entry
Database: PDB / ID: 3s0n
TitleCrystal Structure of Human Chymase with Benzimidazolone Inhibitor
ComponentsChymase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


chymase / basement membrane disassembly / cytokine precursor processing / midbrain development / Activation of Matrix Metalloproteinases / angiotensin maturation / extracellular matrix disassembly / Metabolism of Angiotensinogen to Angiotensins / serine-type peptidase activity / secretory granule ...chymase / basement membrane disassembly / cytokine precursor processing / midbrain development / Activation of Matrix Metalloproteinases / angiotensin maturation / extracellular matrix disassembly / Metabolism of Angiotensinogen to Angiotensins / serine-type peptidase activity / secretory granule / cellular response to glucose stimulus / peptide binding / protein catabolic process / Signaling by SCF-KIT / cytoplasmic ribonucleoprotein granule / positive regulation of angiogenesis / regulation of inflammatory response / collagen-containing extracellular matrix / endopeptidase activity / serine-type endopeptidase activity / intracellular membrane-bounded organelle / extracellular space / extracellular region / cytosol / cytoplasm
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsQian, K.C. / Farrow, N.A. / Padyana, A.K.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Benzimidazolone as potent chymase inhibitor: Modulation of reactive metabolite formation in the hydrophobic (P(1)) region.
Authors: Lo, H.Y. / Nemoto, P.A. / Kim, J.M. / Hao, M.H. / Qian, K.C. / Farrow, N.A. / Albaugh, D.R. / Fowler, D.M. / Schneiderman, R.D. / Michael August, E. / Martin, L. / Hill-Drzewi, M. / Pullen, ...Authors: Lo, H.Y. / Nemoto, P.A. / Kim, J.M. / Hao, M.H. / Qian, K.C. / Farrow, N.A. / Albaugh, D.R. / Fowler, D.M. / Schneiderman, R.D. / Michael August, E. / Martin, L. / Hill-Drzewi, M. / Pullen, S.S. / Takahashi, H. / De Lombaert, S.
History
DepositionMay 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chymase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8805
Polymers24,9921
Non-polymers8884
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.830, 73.830, 48.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Chymase / / Alpha-chymase / Mast cell protease I


Mass: 24991.857 Da / Num. of mol.: 1 / Fragment: UNP residues 22-247 / Mutation: F127K,V208A,R235Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CMA1, CYH, CYM / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P23946, chymase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-0BB / 4-{3-[(4-methyl-1-benzothiophen-3-yl)methyl]-2-oxo-2,3-dihydro-1H-benzimidazol-1-yl}butanoic acid


Mass: 380.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20N2O3S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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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: 2.64 Å3/Da / Density % sol: 53.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 8
Details: 26 - 33% PEG8000, 0.1 M Tris pH 8.0, 2 mM ZnSO4 , VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 1, 2005 / Details: OSMIC Mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 19257 / Num. obs: 18933 / % possible obs: 98.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.101 / Χ2: 1.614 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-1.983.20.4798931.063195.4
1.98-2.023.30.4119201.041194.9
2.02-2.063.30.4029411.127198.7
2.06-2.13.40.3669391.153196.6
2.1-2.153.50.3259211.197198.3
2.15-2.23.50.2899171.192197.3
2.2-2.253.50.279541.166198.9
2.25-2.313.50.2379261.193197.7
2.31-2.383.60.2099601.331199.4
2.38-2.463.60.2049481.302198.3
2.46-2.543.60.1819521.331199
2.54-2.653.60.1629491.362199.5
2.65-2.773.60.1529441.436199.2
2.77-2.913.60.1299521.578199.6
2.91-3.13.60.1099731.782199.7
3.1-3.333.60.0869532.119199.7
3.33-3.673.60.079852.473199.9
3.67-4.23.60.0589602.776199.8
4.2-5.293.60.0529802.782199.7
5.29-503.40.0469662.43195.2

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
CNXphasing
CNXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PJP

1pjp


Resolution: 1.95→15.63 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2296 873 4.5 %RANDOM
Rwork0.1926 17205 --
all-19204 --
obs-18078 94.1 %-
Displacement parametersBiso max: 80.82 Å2 / Biso mean: 26.9702 Å2 / Biso min: 2.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.072 Å20 Å20 Å2
2---0.072 Å20 Å2
3---0.144 Å2
Refinement stepCycle: LAST / Resolution: 1.95→15.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 56 171 1982
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3981.5
X-RAY DIFFRACTIONc_scbond_it2.242
X-RAY DIFFRACTIONc_mcangle_it2.2262
X-RAY DIFFRACTIONc_scangle_it3.3062.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2carbohydrate.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5bi2.par

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