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- PDB-1biw: DESIGN AND SYNTHESIS OF CONFORMATIONALLY-CONSTRAINED MMP INHIBITORS -

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Basic information

Entry
Database: PDB / ID: 1biw
TitleDESIGN AND SYNTHESIS OF CONFORMATIONALLY-CONSTRAINED MMP INHIBITORS
ComponentsPROTEIN (STROMELYSIN-1 COMPLEX)
KeywordsHYDROLASE / STROMELYSIN / MATRIX METALLOPROTEASE / OSTEOARTHRITIS / STRUCTURE-BASED DRUG DESIGN / PROTEIN CRYSTAL STRUCTURE
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 / negative regulation of reactive oxygen species metabolic process / extracellular matrix disassembly ...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 / negative regulation of reactive oxygen species metabolic process / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix organization / EGFR Transactivation by Gastrin / extracellular matrix / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to nitric oxide / regulation of cell migration / cellular response to reactive oxygen species / cellular response to amino acid stimulus / positive regulation of protein-containing complex assembly / protein catabolic process / metalloendopeptidase activity / metallopeptidase activity / peptidase activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / Extra-nuclear estrogen signaling / innate immune response / serine-type endopeptidase activity / mitochondrion / proteolysis / extracellular space / extracellular region / zinc ion binding / nucleus / cytosol
Similarity search - Function
Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Putative peptidoglycan binding domain ...Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Putative peptidoglycan binding domain / 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-S80 / Stromelysin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsNatchus, M.G. / Cheng, M. / Wahl, C.T. / Pikul, S. / Almstead, N.G. / Bradley, R.S. / Taiwo, Y.O. / Mieling, G.E. / Dunaway, C.M. / Snider, C.E. ...Natchus, M.G. / Cheng, M. / Wahl, C.T. / Pikul, S. / Almstead, N.G. / Bradley, R.S. / Taiwo, Y.O. / Mieling, G.E. / Dunaway, C.M. / Snider, C.E. / McIver, J.M. / Barnett, B.L. / McPhail, S.J. / Anastasio, M.B. / De, B.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 1998
Title: Design and synthesis of conformationally-constrained MMP inhibitors.
Authors: Natchus, M.G. / Cheng, M. / Wahl, C.T. / Pikul, S. / Almstead, N.G. / Bradley, R.S. / Taiwo, Y.O. / Mieling, G.E. / Dunaway, C.M. / Snider, C.E. / McIver, J.M. / Barnett, B.L. / McPhail, S.J. ...Authors: Natchus, M.G. / Cheng, M. / Wahl, C.T. / Pikul, S. / Almstead, N.G. / Bradley, R.S. / Taiwo, Y.O. / Mieling, G.E. / Dunaway, C.M. / Snider, C.E. / McIver, J.M. / Barnett, B.L. / McPhail, S.J. / Anastasio, M.B. / De, B.
History
DepositionJun 19, 1998Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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

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Assembly

Deposited unit
A: PROTEIN (STROMELYSIN-1 COMPLEX)
B: PROTEIN (STROMELYSIN-1 COMPLEX)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,75113
Polymers38,8332
Non-polymers91811
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.060, 77.280, 106.400
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 PROTEIN (STROMELYSIN-1 COMPLEX) / MMP3


Mass: 19416.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: COMPLEXED TO PGV-25680 / 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-S80 / N1-HYDROXY-2-(3-HYDROXY-PROPYL)-3-ISOBUTYL-N4-[1-(2-METHOXY-ETHYL)-2-OXO-AZEPAN-3-YL]-SUCCINAMIDE / A DISUBSTITUTED SUCCINYL CAPROLACTAM HYDROXYMATE MMP3 INHIBITOR


Mass: 415.524 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H37N3O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.01 Å3/Da / Density % sol: 38.95 %
Crystal growpH: 7.5
Details: 10 MG/ML PROTEIN IN 20-24% PEG 8000, 2.5% 2-PROPANOL, 10MM CACL2 AND 0.1M TRIS HCL BUFFER, PH 7.5-8.0
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. obs: 11630 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rmerge(I) obs: 0.08 / Rsym value: 0.1 / Net I/σ(I): 11

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementResolution: 2.5→8 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.275 981 10 %RANDOM
Rwork0.247 ---
obs0.247 ---
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2723 0 39 52 2814
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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