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- PDB-1bqo: DISCOVERY OF POTENT, ACHIRAL MATRIX METALLOPROTEINASE INHIBITORS -

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Basic information

Entry
Database: PDB / ID: 1bqo
TitleDISCOVERY OF POTENT, ACHIRAL MATRIX METALLOPROTEINASE INHIBITORS
ComponentsSTROMELYSIN-1Matrix metalloproteinase
KeywordsMETALLOPROTEASE / STROMELYSIN / MATRIX METALLOPROTEASE / OSTEOARTHRITIS / STRUCTURE-BASED DRUG DESIGN
Function / homology
Function and homology information


stromelysin 1 / cellular response to UV-A / regulation of neuroinflammatory response / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / cellular response to nitric oxide ...stromelysin 1 / cellular response to UV-A / regulation of neuroinflammatory response / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / cellular response to nitric oxide / negative regulation of reactive oxygen species metabolic process / EGFR Transactivation by Gastrin / extracellular matrix / Degradation of the extracellular matrix / extracellular matrix organization / positive regulation of protein-containing complex assembly / metalloendopeptidase activity / cellular response to reactive oxygen species / metallopeptidase activity / peptidase activity / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / cellular response to lipopolysaccharide / Extra-nuclear estrogen signaling / serine-type endopeptidase activity / innate immune response / proteolysis / extracellular space / zinc ion binding / extracellular region / nucleus / cytoplasm
Similarity search - Function
Peptidoglycan binding-like / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin ...Peptidoglycan binding-like / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Hemopexin repeat profile. / Hemopexin-like repeats. / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / PGBD-like superfamily / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-N25 / Stromelysin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsPikul, S. / Dunham, K.L.M. / Almstead, N.G. / De, B. / Natchus, M.G. / Anastasio, M.V. / Mcphail, S.J. / Snider, C.E. / Taiwo, Y.O. / Rydel, T.J. ...Pikul, S. / Dunham, K.L.M. / Almstead, N.G. / De, B. / Natchus, M.G. / Anastasio, M.V. / Mcphail, S.J. / Snider, C.E. / Taiwo, Y.O. / Rydel, T.J. / Dunaway, C.M. / Gu, F. / Mieling, G.E.
CitationJournal: J.Med.Chem. / Year: 1998
Title: Discovery of potent, achiral matrix metalloproteinase inhibitors.
Authors: Pikul, S. / McDow Dunham, K.L. / Almstead, N.G. / De, B. / Natchus, M.G. / Anastasio, M.V. / McPhail, S.J. / Snider, C.E. / Taiwo, Y.O. / Rydel, T. / Dunaway, C.M. / Gu, F. / Mieling, G.E.
History
DepositionAug 17, 1998Processing site: BNL
Revision 1.0Aug 17, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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 / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STROMELYSIN-1
B: STROMELYSIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,84913
Polymers38,8332
Non-polymers1,01611
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: STROMELYSIN-1
hetero molecules

B: STROMELYSIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,84913
Polymers38,8332
Non-polymers1,01611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_464-x-1/2,-y+1,z-1/21
Buried area2570 Å2
ΔGint-139 kcal/mol
Surface area16780 Å2
MethodPISA
3
B: STROMELYSIN-1
hetero molecules

A: STROMELYSIN-1
B: STROMELYSIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,03020
Polymers58,2503
Non-polymers1,78017
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation2_464-x-1/2,-y+1,z-1/21
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)37.900, 79.000, 106.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein STROMELYSIN-1 / Matrix metalloproteinase / MMP-3


Mass: 19416.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: COMPLEXED TO PG-117025 / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P08254, stromelysin 1
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-N25 / 1,3-BIS-(4-METHOXY-BENZENESULFONYL)-5,5-DIMETHYL-HEXAHYDRO-PYRIMIDINE-2-CARBOXYLIC ACID HYDROXYAMIDE


Mass: 513.584 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N3O8S2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 14328 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 9 % / Rmerge(I) obs: 0.09

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.81refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementResolution: 2.3→6 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.294 -10 %RANDOM
Rwork0.229 ---
obs0.229 14328 96.5 %-
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2722 0 44 75 2841
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARHCSDX.PRO
X-RAY DIFFRACTION2

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