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(-) Description

Title :  THE DISCOVERY OF MMP7 INHIBITORS EXPLOITING A NOVEL SELECTIVITY TRIGGER
 
Authors :  K. Edman, M. Furber, P. Hemsley, C. Johansson, G. Pairaudeau, J. Peters M. Stocks, A. Tervo, A. Ward, E. Wells, L. Wissler
Date :  20 Jan 11  (Deposition) - 04 May 11  (Release) - 04 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Edman, M. Furber, P. Hemsley, C. Johansson, G. Pairaudeau, J. Petersen, M. Stocks, A. Tervo, A. Ward, E. Wells, L. Wissler
The Discovery Of Mmp7 Inhibitors Exploiting A Novel Selectivity Trigger.
Chemmedchem V. 6 769 2011
PubMed-ID: 21520417  |  Reference-DOI: 10.1002/CMDC.201000550

(-) Compounds

Molecule 1 - MATRILYSIN
    ChainsA
    EC Number3.4.24.23
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMATRIN, MATRIX METALLOPROTEINASE-7, MMP-7, PUMP-1 PROTEASE, UTERINE METALLOPROTEINASE, MMP7

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (4x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2SO42Ligand/IonSULFATE ION
3TQJ1Ligand/IonN-[(2S)-1-[4-(5-BROMOPYRIDIN-2-YL)PIPERAZIN-1-YL]SULFONYL-5-PYRIMIDIN-2-YL-PENTAN-2-YL]-N-HYDROXY-METHANAMIDE
4ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2SO48Ligand/IonSULFATE ION
3TQJ4Ligand/IonN-[(2S)-1-[4-(5-BROMOPYRIDIN-2-YL)PIPERAZIN-1-YL]SULFONYL-5-PYRIMIDIN-2-YL-PENTAN-2-YL]-N-HYDROXY-METHANAMIDE
4ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:175 , GLY A:176 , GLY A:178 , THR A:180 , ASP A:198 , GLU A:201BINDING SITE FOR RESIDUE CA A1265
2AC2SOFTWAREASP A:158 , GLY A:190 , GLY A:192 , ASP A:194 , HOH A:2043 , HOH A:2061BINDING SITE FOR RESIDUE CA A1266
3AC3SOFTWAREHIS A:168 , ASP A:170 , HIS A:183 , HIS A:196BINDING SITE FOR RESIDUE ZN A1267
4AC4SOFTWAREHIS A:219 , HIS A:223 , HIS A:229 , TQJ A:1271BINDING SITE FOR RESIDUE ZN A1268
5AC5SOFTWAREPRO A:126 , HIS A:127 , ILE A:128 , ASN A:234 , HOH A:2100 , HOH A:2101BINDING SITE FOR RESIDUE SO4 A1269
6AC6SOFTWAREASN A:234 , SER A:252 , GLN A:253 , HOH A:2087 , HOH A:2101 , HOH A:2102BINDING SITE FOR RESIDUE SO4 A1270
7AC7SOFTWARETYR A:172 , LEU A:181 , ALA A:182 , HIS A:183 , TYR A:215 , HIS A:219 , GLU A:220 , HIS A:223 , HIS A:229 , VAL A:236 , TYR A:238 , PRO A:239 , THR A:240 , TYR A:241 , ZN A:1268 , HOH A:2057 , HOH A:2103 , HOH A:2104BINDING SITE FOR RESIDUE TQJ A1271

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y6D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Y6D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_021027G137DMMP7_HUMANPolymorphism17884789AG142D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_021027G137DMMP7_HUMANPolymorphism17884789AG142D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.MMP7_HUMAN211-220  1A:216-225
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.MMP7_HUMAN211-220  4A:216-225

(-) Exons   (5, 5)

Asymmetric Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002602271aENSE00002145134chr11:102401484-102401324161MMP7_HUMAN1-36360--
1.2ENST000002602272ENSE00000930299chr11:102398714-102398488227MMP7_HUMAN37-112761A:99-11719
1.3aENST000002602273aENSE00000930298chr11:102398403-102398255149MMP7_HUMAN112-162511A:117-16751
1.4aENST000002602274aENSE00000930297chr11:102395795-102395667129MMP7_HUMAN162-205441A:167-21044
1.5ENST000002602275ENSE00000930296chr11:102394132-102393971162MMP7_HUMAN205-259551A:210-264 (gaps)55
1.6ENST000002602276ENSE00001252223chr11:102391535-102391239297MMP7_HUMAN259-26791A:264-2641

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:160
 aligned with MMP7_HUMAN | P09237 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:166
                                   103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253      
           MMP7_HUMAN    94 EYSLFPNSPKWTSKVVTYRIVSYTRDLPHITVDRLVSKALNMWGKEIPLHFRKVVWGTADIMIGFARGAHGDSYPFDGPGNTLAHAFAPGTGLGGDAHFDEDERWTDGSSLGINFLYAATHELGHSLGMGHSSDPNAVMYPTYGNGDPQNFKLSQDDIKGIQKLYG 259
               SCOP domains d2y6da_ A: automated matches                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------Peptidase_M10-2y6dA01 A:108-264                                                                                                                               Pfam domains
         Sec.struct. author ..............eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee......eehhhhhhhhhhhhh................------....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------D-------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------ZINC_PROTE--------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2           -------------------------------------------------Exon 1.4a  PDB: A:167-210 UniProt: 162-205  -----------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) ------------------Exon 1.3a  PDB: A:117-167 UniProt: 112-162         ------------------------------------------Exon 1.5  PDB: A:210-264 (gaps) UniProt: 205-259        Transcript 1 (2)
                 2y6d A  99 GYSLFPNSPKWTSKVVTYRIVSYTRDLPHITVDRLVSKALNMWGKEIPLHFRKVVWGTADIMIGFARGAHGDSYPFDGPGNTLAHAFAPGTGLGGDAHFDEDERWTDGSSLGINFLYAATHELGHSLGMGHSSDPNAVMYPTY------NFKLSQDDIKGIQKLYG 264
                                   108       118       128       138       148       158       168       178       188       198       208       218       228       238  |    248       258      
                                                                                                                                                                        241    248                

   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y6D)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A   (MMP7_HUMAN | P09237)
molecular function
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0071260    cellular response to mechanical stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
    GO:0030574    collagen catabolic process    The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells.
    GO:0044849    estrous cycle    A type of ovulation cycle, which occurs in most mammalian therian females, where the endometrium is resorbed if pregnancy does not occur.
    GO:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    GO:0060135    maternal process involved in female pregnancy    A reproductive process occurring in the mother that allows an embryo or fetus to develop within it.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0031667    response to nutrient levels    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of nutrients.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005578    proteinaceous extracellular matrix    A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MMP7_HUMAN | P092371mmp 1mmq 1mmr 2ddy 2mze 2mzh 2mzi 2y6c

(-) Related Entries Specified in the PDB File

1mmp MATRILYSIN COMPLEXED WITH CARBOXYLATE INHIBITOR
1mmq MATRILYSIN COMPLEXED WITH HYDROXAMATE INHIBITOR
1mmr MATRILYSIN COMPLEXED WITH SULFODIIMINE INHIBITOR
2y6c THE DISCOVERY OF MMP7 INHIBITORS EXPLOITING A NOVEL SELECTIVITY TRIGGER