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- PDB-9gbh: CRYSTAL STRUCTURE OF HUMAN CHYMASE IN COMPLEX WITH COMPOUND1 -

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Basic information

Entry
Database: PDB / ID: 9gbh
TitleCRYSTAL STRUCTURE OF HUMAN CHYMASE IN COMPLEX WITH COMPOUND1
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 / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / serine-type peptidase activity ...chymase / basement membrane disassembly / cytokine precursor processing / peptide metabolic process / midbrain development / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / serine-type peptidase activity / protein maturation / 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 / : / 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: 2.375 Å
AuthorsSchaefer, M. / Fuerstner, C. / Ackerstaff, J. / Meier, H. / Straub, A. / Mittendorf, J. / Schamberger, J. / Boerngen, K. / Joerissen, H. / Zubow, D. ...Schaefer, M. / Fuerstner, C. / Ackerstaff, J. / Meier, H. / Straub, A. / Mittendorf, J. / Schamberger, J. / Boerngen, K. / Joerissen, H. / Zubow, D. / Zimmermann, K. / Tersteegen, A. / Geiss, V. / Hartmann, E. / Albrecht-Kuepper, B. / Dorleans-Juste, P. / Lapointe, C. / Vincent, L. / Heitmeier, S. / Tinel, H.
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
DepositionJul 31, 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

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Assembly

Deposited unit
AAA: Chymase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2006
Polymers25,0201
Non-polymers1,1805
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-13 kcal/mol
Surface area10990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.093, 74.093, 49.647
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: 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
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / 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
#3: Chemical ChemComp-A1IJV / 2-(3,4-dimethoxyphenyl)-3,5-bis(oxidanylidene)-4-[[3-(trifluoromethyl)phenyl]methyl]-1,2,4-triazine-6-carboxylic acid


Mass: 451.353 Da / Num. of mol.: 1 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
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: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / 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: Apr 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.36→37.04 Å / Num. obs: 574082 / % possible obs: 97.49 % / Redundancy: 13.85 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 4.5929
Reflection shellResolution: 2.36→2.49 Å / Rmerge(I) obs: 0.27 / Num. unique obs: 18908

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.375→37.04 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.713 / Cross valid method: FREE R-VALUE / ESU R: 0.39 / ESU R Free: 0.281
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.274 528 4.806 %
Rwork0.2021 10459 -
all0.206 --
obs-10987 99.592 %
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: 43.315 Å2
Baniso -1Baniso -2Baniso -3
1--0.253 Å20 Å2-0 Å2
2---0.253 Å2-0 Å2
3---0.506 Å2
Refinement stepCycle: LAST / Resolution: 2.375→37.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1666 0 75 126 1867
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121795
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.7012426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4935215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.85720.83384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01915300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8571513
X-RAY DIFFRACTIONr_chiral_restr0.0720.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021317
X-RAY DIFFRACTIONr_nbd_refined0.2760.2734
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21197
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2108
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2310.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1280.213
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0740.21
X-RAY DIFFRACTIONr_mcbond_it3.033.993860
X-RAY DIFFRACTIONr_mcangle_it4.1785.9831069
X-RAY DIFFRACTIONr_scbond_it4.1514.56935
X-RAY DIFFRACTIONr_scangle_it6.3166.6321355
X-RAY DIFFRACTIONr_lrange_it7.46655.282630
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.375-2.4370.316320.179763X-RAY DIFFRACTION97.786
2.437-2.5030.308260.17743X-RAY DIFFRACTION99.354
2.503-2.5750.248400.178730X-RAY DIFFRACTION100
2.575-2.6540.318460.18687X-RAY DIFFRACTION99.7279
2.654-2.7410.295340.184682X-RAY DIFFRACTION100
2.741-2.8360.248330.165666X-RAY DIFFRACTION99.8571
2.836-2.9430.236350.167641X-RAY DIFFRACTION100
2.943-3.0620.272310.167618X-RAY DIFFRACTION100
3.062-3.1970.342260.173598X-RAY DIFFRACTION99.84
3.197-3.3520.264380.203556X-RAY DIFFRACTION100
3.352-3.5320.26270.249559X-RAY DIFFRACTION99.8296
3.532-3.7440.222230.292506X-RAY DIFFRACTION99.8113
3.744-40.487190.293462X-RAY DIFFRACTION97.3684
4-4.3160.247140.192463X-RAY DIFFRACTION100
4.316-4.7220.258290.161406X-RAY DIFFRACTION100
4.722-5.2680.165180.164388X-RAY DIFFRACTION100
5.268-6.0630.252150.187334X-RAY DIFFRACTION100
6.063-7.3760.176160.205289X-RAY DIFFRACTION100
7.376-10.2310.283120.175231X-RAY DIFFRACTION100
10.231-37.040.183140.291137X-RAY DIFFRACTION100

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