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(-) Description

Title :  A CARBOXYLIC ACID BASED INHIBITOR IN COMPLEX WITH MMP3
 
Authors :  M. G. Natchus, R. G. Bookland, M. J. Laufersweiler, S. Pikul, N. G. Almst M. J. Janusz, L. C. Hsieh, F. Gu, M. E. Pokross, V. S. Patel, S. M. Garver, T. M. Branch, S. L. King, T. R. Baker, D. J. Foltz, G. E. Mieling
Date :  18 Jan 01  (Deposition) - 18 Jan 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Biol. Unit 4:  A,B  (1x)
Keywords :  Mixed Alpha Beta Structure, Zinc Protease, Inhibited, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. G. Natchus, R. G. Bookland, M. J. Laufersweiler, S. Pikul, N. G. Almstead, B. De, M. J. Janusz, L. C. Hsieh, F. Gu, M. E. Pokross, V. S. Patel, S. M. Garver, S. X. Peng, T. M. Branch, S. L. King, T. R. Baker D. J. Foltz, G. E. Mieling
Development Of New Carboxylic Acid-Based Mmp Inhibitors Derived From Functionalized Propargylglycines.
J. Med. Chem. V. 44 1060 2001
PubMed-ID: 11297453  |  Reference-DOI: 10.1021/JM000477L

(-) Compounds

Molecule 1 - STROMELYSIN-1
    CellFIBROBLAST
    ChainsA, B
    EC Number3.4.24.17
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentCATALYTIC DOMAIN, RESIDUES 100-272
    GeneMMP3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMMP-3

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (1x)A (1x)B (1x)
Biological Unit 4 (1x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2MBS1Ligand/IonR-2-{[4'-METHOXY-(1,1'-BIPHENYL)-4-YL]-SULFONYL}-AMINO-6-METHOXY-HEX-4-YNOIC ACID
3ZN4Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MBS-1Ligand/IonR-2-{[4'-METHOXY-(1,1'-BIPHENYL)-4-YL]-SULFONYL}-AMINO-6-METHOXY-HEX-4-YNOIC ACID
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MBS1Ligand/IonR-2-{[4'-METHOXY-(1,1'-BIPHENYL)-4-YL]-SULFONYL}-AMINO-6-METHOXY-HEX-4-YNOIC ACID
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MBS-1Ligand/IonR-2-{[4'-METHOXY-(1,1'-BIPHENYL)-4-YL]-SULFONYL}-AMINO-6-METHOXY-HEX-4-YNOIC ACID
3ZN-1Ligand/IonZINC ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MBS1Ligand/IonR-2-{[4'-METHOXY-(1,1'-BIPHENYL)-4-YL]-SULFONYL}-AMINO-6-METHOXY-HEX-4-YNOIC ACID
3ZN-1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:201 , HIS A:205 , HIS A:211 , HOH A:379 , THR B:755BINDING SITE FOR RESIDUE ZN A 301
02AC2SOFTWAREHIS A:151 , ASP A:153 , HIS A:166 , HIS A:179BINDING SITE FOR RESIDUE ZN A 302
03AC3SOFTWAREASP A:158 , GLY A:159 , GLY A:161 , VAL A:163 , ASP A:181 , GLU A:184BINDING SITE FOR RESIDUE CA A 303
04AC4SOFTWAREASP A:107 , ASP A:182 , GLU A:184 , HOH A:326 , HOH A:341BINDING SITE FOR RESIDUE CA A 304
05AC5SOFTWAREASP A:141 , GLY A:173 , ASN A:175 , ASP A:177 , HOH A:306 , HOH A:307BINDING SITE FOR RESIDUE CA A 305
06AC6SOFTWAREHIS B:701 , HIS B:705 , HIS B:711 , MBS B:901BINDING SITE FOR RESIDUE ZN B 801
07AC7SOFTWAREHIS B:651 , ASP B:653 , HIS B:666 , HIS B:679BINDING SITE FOR RESIDUE ZN B 802
08AC8SOFTWAREASP B:658 , GLY B:659 , GLY B:661 , VAL B:663 , ASP B:681 , GLU B:684BINDING SITE FOR RESIDUE CA B 803
09AC9SOFTWAREHOH B:20 , HOH B:52 , ASP B:607 , ASP B:682 , GLU B:684BINDING SITE FOR RESIDUE CA B 804
10BC1SOFTWAREHOH B:12 , HOH B:64 , ASP B:641 , GLY B:673 , ASN B:675 , ASP B:677BINDING SITE FOR RESIDUE CA B 805
11BC2SOFTWAREHOH B:76 , HOH B:109 , HOH B:221 , VAL B:663 , LEU B:664 , ALA B:665 , HIS B:666 , LEU B:697 , HIS B:701 , GLU B:702 , HIS B:705 , HIS B:711 , LEU B:718 , TYR B:720 , PRO B:721 , LEU B:722 , ZN B:801BINDING SITE FOR RESIDUE MBS B 901

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1HY7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1HY7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1HY7)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.MMP3_HUMAN215-224
 
  2A:198-207
B:698-707
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.MMP3_HUMAN215-224
 
  1A:198-207
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.MMP3_HUMAN215-224
 
  1-
B:698-707
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.MMP3_HUMAN215-224
 
  2A:198-207
B:698-707
Biological Unit 4 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.MMP3_HUMAN215-224
 
  2A:198-207
B:698-707

(-) Exons   (5, 10)

Asymmetric Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002998551aENSE00002171374chr11:102714534-102714173362MMP3_HUMAN1-35350--
1.2ENST000002998552ENSE00001105428chr11:102713647-102713403245MMP3_HUMAN36-117822A:83-100
B:583-600
18
18
1.3ENST000002998553ENSE00001642002chr11:102713310-102713162149MMP3_HUMAN117-167512A:100-150
B:600-650
51
51
1.4bENST000002998554bENSE00001105420chr11:102713010-102712885126MMP3_HUMAN167-209432A:150-192
B:650-692
43
43
1.5ENST000002998555ENSE00001657829chr11:102711324-102711160165MMP3_HUMAN209-264562A:192-247 (gaps)
B:692-747 (gaps)
56
56
1.6ENST000002998556ENSE00001105427chr11:102710983-102710839145MMP3_HUMAN264-312492A:247-250
B:747-755
4
9
1.7ENST000002998557ENSE00001105439chr11:102709974-102709841134MMP3_HUMAN312-357460--
1.8ENST000002998558ENSE00001801971chr11:102709441-102709282160MMP3_HUMAN357-410540--
1.9ENST000002998559ENSE00001105448chr11:102708132-102708029104MMP3_HUMAN410-445360--
1.11ENST0000029985511ENSE00001292630chr11:102706957-102706532426MMP3_HUMAN445-477330--

(-) 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:162
 aligned with MMP3_HUMAN | P08254 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:168
                                   109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259        
           MMP3_HUMAN   100 FRTFPGIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEADIMISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHEIGHSLGLFHSANTEALMYPLYHSLTDLTRFRLSQDDINGIQSLYGPPP 267
               SCOP domains d1hy7a_ A: Stromelysin-1 (MMP-3)                                                                                                                                         SCOP domains
               CATH domains 1hy7A00 A:83-250 Collagenase (Catalytic Domain)                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhh...............------......hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------ZINC_PROTE------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2          -------------------------------------------------Exon 1.4b  PDB: A:150-192 UniProt: 167-209 ------------------------------------------------------1.6  Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.3  PDB: A:100-150 UniProt: 117-167          -----------------------------------------Exon 1.5  PDB: A:192-247 (gaps) UniProt: 209-264        --- Transcript 1 (2)
                 1hy7 A  83 FRTFPGIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEADIMISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHEIGHSLGLFHSANTEALMYPL------LTRFRLSQDDINGIQSLYGPPP 250
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222      |232       242        
                                                                                                                                                                     222    229                     

Chain B from PDB  Type:PROTEIN  Length:171
 aligned with MMP3_HUMAN | P08254 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:173
                                   109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269   
           MMP3_HUMAN   100 FRTFPGIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEADIMISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHEIGHSLGLFHSANTEALMYPLYHSLTDLTRFRLSQDDINGIQSLYGPPPDSPET 272
               SCOP domains d1hy7b_ B: Stromelysin-1 (MMP-3)                                                                                                                                              SCOP domains
               CATH domains 1hy7B00 B:583-755 Collagenase (Catalytic Domain)                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhh................--..hhhhh..hhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------ZINC_PROTE------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.2          -------------------------------------------------Exon 1.4b  PDB: B:650-692 UniProt: 167-209 ------------------------------------------------------Exon 1.6  Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.3  PDB: B:600-650 UniProt: 117-167          -----------------------------------------Exon 1.5  PDB: B:692-747 (gaps) UniProt: 209-264        -------- Transcript 1 (2)
                 1hy7 B 583 FRTFPGIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEADIMISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHEIGHSLGLFHSANTEALMYPLY--LTDLTRFRLSQDDINGIQSLYGPPPDSPET 755
                                   592       602       612       622       632       642       652       662       672       682       692       702       712       722|  |   732       742       752   
                                                                                                                                                                      723  |                             
                                                                                                                                                                         726                             

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HY7)

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MMP3_HUMAN | P08254)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0071732    cellular response to nitric oxide    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 nitric oxide 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:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    GO:0010727    negative regulation of hydrogen peroxide metabolic process    Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving hydrogen peroxide.
    GO:1903209    positive regulation of oxidative stress-induced cell death    Any process that activates or increases the frequency, rate or extent of oxidative stress-induced cell death.
    GO:0032461    positive regulation of protein oligomerization    Any process that activates or increases the frequency, rate or extent of protein oligomerization.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    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
        MMP3_HUMAN | P082541b3d 1b8y 1biw 1bm6 1bqo 1c3i 1c8t 1caq 1ciz 1cqr 1d5j 1d7x 1d8f 1d8m 1g05 1g49 1g4k 1hfs 1m1w 1oo9 1qia 1qic 1slm 1sln 1uea 1ums 1umt 1usn 2d1o 2jnp 2jt5 2jt6 2srt 2usn 3ohl 3oho 3usn 4dpe 4g9l 4ja1

(-) Related Entries Specified in the PDB File

1cqr CRYSTAL STRUCTURE OF THE STROMELYSIN CATALYTIC DOMAIN AT 2.0 A RESOLUTION
1d5j CRYSTAL STRUCTURE OF MMP3 COMPLEXED WITH A THIAZEPINE BASED INHIBITOR
1d7x CRYSTAL STRUCTURE OF MMP3 COMPLEXED WITH A MODIFIED PROLINE SCAFFOLD BASED INHIBITOR
1d8f CRYSTAL STRUCTURE OF MMP3 COMPLEXED WITH A PIPERAZINE BASED INHIBITOR
1d8m CRYSTAL STRUCTURE OF MMP3 COMPLEXED WITH A HETEROCYCLE- BASED INHIBITOR
1g49 A CARBOXYLIC ACID BASED INHIBITOR IN COMPLEX WITH MMP3