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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF MMP-13 COMPLEXED WITH 4-OXO-N-(3-(2-(1H-1,2,4-TRIAZOL-3-YLSULFANYL)ETHOXY)BENZYL)-3,4-DIHYDROQUINAZOLINE-2-CARBOXAMIDE
 
Authors :  H. Oki, Y. Tanaka
Date :  13 May 16  (Deposition) - 18 Jan 17  (Release) - 08 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Mmp-13, Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Nara, A. Kaieda, K. Sato, T. Naito, H. Mototani, H. Oki, Y. Yamamoto, H. Kuno, T. Santou, N. Kanzaki, J. Terauchi, O. Uchikawa, M. Kori
Discovery Of Novel, Highly Potent, And Selective Matrix Metalloproteinase (Mmp)-13 Inhibitors With A 1, 2, 4-Triazol-3-Yl Moiety As A Zinc Binding Group Using A Structure-Based Design Approach
J. Med. Chem. V. 60 608 2017
PubMed-ID: 27966948  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B01007

(-) Compounds

Molecule 1 - COLLAGENASE 3
    Chains: A, B
    EC Number: 3.4.24.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, RESIDUES 103-274
    Gene: MMP13
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MATRIX METALLOPROTEINASE-13,MMP-13

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2WNN2Ligand/Ion4-OXO-N-{3-[2-(1H-1,2,4-TRIAZOL-3-YLSULFANYL)ETHOXY]BENZYL}-3,4-DIHYDROQUINAZOLINE-2-CARBOXAMIDE
3ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2WNN1Ligand/Ion4-OXO-N-{3-[2-(1H-1,2,4-TRIAZOL-3-YLSULFANYL)ETHOXY]BENZYL}-3,4-DIHYDROQUINAZOLINE-2-CARBOXAMIDE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2WNN1Ligand/Ion4-OXO-N-{3-[2-(1H-1,2,4-TRIAZOL-3-YLSULFANYL)ETHOXY]BENZYL}-3,4-DIHYDROQUINAZOLINE-2-CARBOXAMIDE
3ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:222 , HIS A:226 , HIS A:232 , WNN A:306binding site for residue ZN A 301
02AC2SOFTWAREHIS A:172 , ASP A:174 , HIS A:187 , HIS A:200binding site for residue ZN A 302
03AC3SOFTWAREASP A:179 , GLY A:180 , SER A:182 , LEU A:184 , ASP A:202 , GLU A:205binding site for residue CA A 303
04AC4SOFTWAREASP A:162 , ASN A:194 , GLY A:196 , ASP A:198 , HOH A:408 , HOH A:447binding site for residue CA A 304
05AC5SOFTWAREASP A:128 , ASP A:203 , GLU A:205 , HOH B:548binding site for residue CA A 305
06AC6SOFTWAREALA A:186 , LEU A:218 , HIS A:222 , GLU A:223 , HIS A:226 , HIS A:232 , ALA A:238 , LEU A:239 , PHE A:241 , PRO A:242 , ILE A:243 , TYR A:244 , THR A:245 , THR A:247 , PHE A:252 , MET A:253 , ZN A:301 , HOH A:526binding site for residue WNN A 306
07AC7SOFTWAREHIS B:222 , HIS B:226 , HIS B:232 , WNN 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:179 , GLY B:180 , SER B:182 , LEU B:184 , ASP B:202 , GLU B:205binding site for residue CA B 303
10AD1SOFTWAREASP B:162 , ASN B:194 , GLY B:196 , ASP B:198 , HOH B:433 , HOH B:489binding site for residue CA B 304
11AD2SOFTWAREHOH A:566 , ASP B:128 , ASP B:203 , GLU B:205binding site for residue CA B 305
12AD3SOFTWARELEU 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 , PRO B:242 , ILE B:243 , TYR B:244 , THR B:245 , THR B:247 , PHE B:252 , ZN B:301 , HOH B:427 , HOH B:512 , HOH B:531binding site for residue WNN B 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5B5P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5B5P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5B5P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5B5P)

(-) Exons   (0, 0)

(no "Exon" information available for 5B5P)

(-) 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:167
                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee.......hhhhhhhhhhhhhhhhhh....eeeee......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhh........................hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b5p A 104 YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGHFMLPDDDVQGIQSLYGPGDED 272
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243    || 255       265       
                                                                                                                                                                          248|                     
                                                                                                                                                                           251                     


Chain B from PDB  Type:PROTEIN  Length:165
                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 5b5p B 104 YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGP 268
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263
   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  (0, 0)

(no "SCOP Domain" information available for 5B5P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5B5P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5B5P)

(-) Gene Ontology  (42, 42)

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  3.4.24.-
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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 4jpa 4l19 5b5o 5bot 5boy 5bpa 5uwk 5uwl 5uwm 5uwn 830c

(-) Related Entries Specified in the PDB File

3wv1 3wv2 3wv3 5b5o