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- PDB-9gc9: CRYSTAL STRUCTURE OF HUMAN CHYMASE IN COMPLEX WITH COMPOUND27 -

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Basic information

Entry
Database: PDB / ID: 9gc9
TitleCRYSTAL STRUCTURE OF HUMAN CHYMASE IN COMPLEX WITH COMPOUND27
ComponentsChymase
KeywordsHYDROLASE / SERINE PROTEASE / GLYCOSYLATED / MAST CELLS / SECRETED / HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


chymase / basement membrane disassembly / cytokine precursor processing / peptide metabolic process / midbrain development / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / protein maturation / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins ...chymase / basement membrane disassembly / cytokine precursor processing / peptide metabolic process / midbrain development / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / protein maturation / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / serine-type peptidase activity / peptide binding / secretory granule / protein catabolic process / cellular response to glucose stimulus / 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 / extracellular space / extracellular region / cytosol
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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.203 Å
AuthorsSchaefer, M. / Fuerstner, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2025
Title: Discovery and Preclinical Characterization of Fulacimstat (BAY 1142524), a Potent and Selective Chymase Inhibitor As a New Profibrinolytic Approach for Safe Thrombus Resolution.
Authors: Furstner, C. / Ackerstaff, J. / Meier, H. / Straub, A. / Mittendorf, J. / Schamberger, J. / Schafer, M. / Borngen, K. / Jorissen, H. / Zubov, D. / Zimmermann, K. / Tersteegen, A. / Geiss, V. ...Authors: Furstner, C. / Ackerstaff, J. / Meier, H. / Straub, A. / Mittendorf, J. / Schamberger, J. / Schafer, M. / Borngen, K. / Jorissen, H. / Zubov, D. / Zimmermann, K. / Tersteegen, A. / Geiss, V. / Hartmann, E. / Albrecht-Kupper, B. / D'Orleans-Juste, P. / Lapointe, C. / Vincent, L. / Heitmeier, S. / Tinel, H.
History
DepositionAug 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Chymase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2195
Polymers25,0201
Non-polymers1,1994
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-13 kcal/mol
Surface area10760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.935, 73.935, 48.909
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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Protein , 1 types, 1 molecules AAA

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


Mass: 25019.871 Da / Num. of mol.: 1 / Mutation: F127K, V208A, R235Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CMA1, CYH, CYM
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: P23946, chymase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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

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Non-polymers , 3 types, 216 molecules

#4: Chemical ChemComp-A1IJ3 / 3-[[2-methyl-3-(trifluoromethyl)phenyl]methyl]-2,4-bis(oxidanylidene)-1-[4-(2-oxidanylideneimidazolidin-1-yl)phenyl]pyrimidine-5-carboxylic acid


Mass: 488.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H19F3N4O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.67 Å3/Da / Density % sol: 53.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.01M ZnCl2, 0.1M TRIS at pH 8 and 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.18→35.72 Å / Num. obs: 50369 / % possible obs: 95.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 9.3
Reflection shellResolution: 2.18→2.3 Å / Rmerge(I) obs: 0.455 / Num. unique obs: 1407 / % possible all: 70.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.203→35.716 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.912 / Cross valid method: FREE R-VALUE / ESU R: 0.256 / ESU R Free: 0.211
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2377 658 4.95 %
Rwork0.1775 12634 -
all0.18 --
obs-13292 98.139 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 49.296 Å2
Baniso -1Baniso -2Baniso -3
1--0.453 Å20 Å20 Å2
2---0.453 Å20 Å2
3---0.905 Å2
Refinement stepCycle: LAST / Resolution: 2.203→35.716 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1666 0 78 214 1958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121788
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.7072419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8555212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.97420.83384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45115294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0671513
X-RAY DIFFRACTIONr_chiral_restr0.0660.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.021320
X-RAY DIFFRACTIONr_nbd_refined0.2320.2832
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21194
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2157
X-RAY DIFFRACTIONr_metal_ion_refined0.1660.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2350.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2470.211
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0020.22
X-RAY DIFFRACTIONr_mcbond_it2.4934.5857
X-RAY DIFFRACTIONr_mcangle_it3.5676.7471066
X-RAY DIFFRACTIONr_scbond_it3.8755.144931
X-RAY DIFFRACTIONr_scangle_it6.1157.5021353
X-RAY DIFFRACTIONr_lrange_it8.11564.222754
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.203-2.260.299330.2877150.2889870.7730.80475.78520.279
2.26-2.3220.303560.2579230.2599790.8340.841000.244
2.322-2.3890.304510.2318790.2359300.8260.8751000.212
2.389-2.4620.233530.2288780.2299310.890.8831000.21
2.462-2.5420.311420.2188110.2238530.850.8941000.199
2.542-2.6310.292340.2028280.2058620.850.9091000.18
2.631-2.730.266430.1757830.1798260.9070.9211000.159
2.73-2.8410.21440.1827540.1847980.9310.9241000.165
2.841-2.9660.292320.177290.1757610.8970.9361000.153
2.966-3.110.238320.1597050.1627370.9050.9411000.144
3.11-3.2770.232320.1566600.166920.9360.951000.142
3.277-3.4740.186290.1566270.1586560.9550.9561000.145
3.474-3.7110.193330.1466080.1486410.9420.9631000.14
3.711-4.0050.173400.1495340.1515740.9630.9641000.142
4.005-4.3810.264210.1445160.1475370.9170.9651000.14
4.381-4.8890.243200.1434660.1464860.9380.9621000.141
4.889-5.6280.165190.1554090.1554280.9590.961000.15
5.628-6.8510.235230.1793600.1823830.9460.9611000.175
6.851-9.5150.293190.182740.1872930.9340.9641000.175
9.515-35.7160.27920.2561750.2561780.9190.9599.43820.27

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