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(-) Description

Title :  MMP13 IN COMPLEX WITH A PIPERAZINE HYDANTOIN LIGAND
 
Authors :  S. Gerhardt, D. Hargreaves
Date :  19 Mar 13  (Deposition) - 05 Mar 14  (Release) - 05 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Matrix Metalloprotease, Calcium Binding, Zinc Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. De Savi, D. Waterson, A. Pape, S. Lamont, E. Hadley, M. Mills, K. M. Page, J. Bowyer, R. A. Maciewicz
Hydantoin Based Inhibitors Of Mmp13--Discovery Of Azd6605.
Bioorg. Med. Chem. Lett. V. 23 4705 2013
PubMed-ID: 23810497  |  Reference-DOI: 10.1016/J.BMCL.2013.05.089

(-) Compounds

Molecule 1 - COLLAGENASE 3
    Chains: A, B
    EC Number: 3.4.24.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Common: HUMAN
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 103-274
    Gene: MMP13
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MATRIX METALLOPROTEINASE-13, MMP-13

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1AZ62Ligand/Ion3-[({2-[4-({[(4S)-4-METHYL-2,5-DIOXOIMIDAZOLIDIN-4-YL]METHYL}SULFONYL)PIPERAZIN-1-YL]PYRIMIDIN-5-YL}OXY)METHYL]BENZONITRILE
2CA4Ligand/IonCALCIUM ION
3NA2Ligand/IonSODIUM ION
4ZN4Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:222 , HIS A:226 , HIS A:232 , AZ6 A:306BINDING SITE FOR RESIDUE ZN A 301
02AC2SOFTWAREASP A:162 , ASN A:194 , GLY A:196 , ASP A:198 , HOH A:402 , HOH A:584BINDING SITE FOR RESIDUE CA A 302
03AC3SOFTWAREHIS A:172 , ASP A:174 , HIS A:187 , HIS A:200BINDING SITE FOR RESIDUE ZN A 303
04AC4SOFTWAREASP A:179 , GLY A:180 , SER A:182 , LEU A:184 , ASP A:202 , GLU A:205BINDING SITE FOR RESIDUE CA A 304
05AC5SOFTWAREASP A:128 , ASP A:203 , GLU A:205 , HOH A:526BINDING SITE FOR RESIDUE NA A 305
06AC6SOFTWARELEU A:184 , LEU A:185 , ALA A:186 , HIS A:187 , LEU A:218 , HIS A:222 , GLU A:223 , HIS A:226 , HIS A:232 , GLY A:237 , ALA A:238 , LEU A:239 , PHE A:241 , PRO A:242 , ILE A:243 , TYR A:244 , THR A:245 , TYR A:246 , ZN A:301 , HOH A:445BINDING SITE FOR RESIDUE AZ6 A 306
07AC7SOFTWAREHIS B:222 , HIS B:226 , HIS B:232 , AZ6 B:306BINDING SITE FOR RESIDUE ZN B 301
08AC8SOFTWAREHIS B:172 , ASP B:174 , HIS B:187 , HIS B:200BINDING SITE FOR RESIDUE ZN B 302
09AC9SOFTWAREASP B:162 , ASN B:194 , GLY B:196 , ASP B:198 , HOH B:427 , HOH B:428BINDING SITE FOR RESIDUE CA B 303
10BC1SOFTWAREASP B:179 , GLY B:180 , SER B:182 , LEU B:184 , ASP B:202 , GLU B:205BINDING SITE FOR RESIDUE CA B 304
11BC2SOFTWAREHOH A:529 , ASP B:128 , ASP B:203 , GLU B:205BINDING SITE FOR RESIDUE NA B 305
12BC3SOFTWAREGLY B:183 , LEU B:185 , ALA B:186 , LEU B:218 , HIS B:222 , GLU B:223 , HIS B:226 , HIS B:232 , ALA B:238 , LEU B:239 , PHE B:241 , ILE B:243 , TYR B:244 , THR B:245 , TYR B:246 , THR B:247 , ZN B:301 , HOH B:507 , HOH B:513 , HOH B:560BINDING SITE FOR RESIDUE AZ6 B 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JPA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JPA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JPA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JPA)

(-) Exons   (0, 0)

(no "Exon" information available for 4JPA)

(-) Sequences/Alignments

Asymmetric/Biological 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:165
                                                                                                                                                                                                     
               SCOP domains d4jpaa_ A: Collagenase-3 (MMP-13)                                                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhhh.....................hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jpa A 104 YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYHFMLPDDDVQGIQSLYGPGDED 272
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243  ||   257       267     
                                                                                                                                                                        246|                     
                                                                                                                                                                         251                     


Chain B from PDB  Type:PROTEIN  Length:166
                                                                                                                                                                                                      
               SCOP domains d4jpab_ B: Collagenase-3 (MMP-13)                                                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee.......hhhhhhhhhhhhhhhhhh....eeeee......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhhh.........................hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jpa B 104 YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPG 269
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263
   Legend:   → Mismatch (orange background)
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  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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JPA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JPA)

(-) Gene Ontology  (42, 42)

Asymmetric/Biological Unit(hide GO term definitions)

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  MMP13_HUMAN | P45452
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 Related Entries

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

UniProtKB/Swiss-Prot
        MMP13_HUMAN | P45452: 1eub 1fls 1fm1 1pex 1uc1 1xuc 1xud 1xur 1you 1ztq 2d1n 2e2d 2ow9 2ozr 2pjt 2yig 3elm 3i7g 3i7i 3kec 3kej 3kek 3kry 3ljz 3o2x 3tvc 3wv1 3wv2 3wv3 3zxh 456c 4a7b 4fu4 4fvl 4g0d 4jp4 4l19 5b5o 5b5p 5bot 5boy 5bpa 5uwk 5uwl 5uwm 5uwn 830c

(-) Related Entries Specified in the PDB File

4jp4 MMP13 IN COMPLEX WITH AZD6605