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(-) Description

Title :  VIM-2-1, DISCOVERY OF NOVEL INHIBITOR SCAFFOLDS AGAINST THE METALLO-BETA-LACTAMASE VIM-2 BY SPR BASED FRAGMENT SCREENING
 
Authors :  T. Christopeit, T. J. O. Carlsen, R. Helland, H. K. S. Leiros
Date :  18 Aug 15  (Deposition) - 04 Nov 15  (Release) - 25 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Christopeit, T. J. O. Carlsen, R. Helland, H. K. S. Leiros
Discovery Of Novel Inhibitor Scaffolds Against The Metallo-Beta-Lactamase Vim-2 By Spr Based Fragment Screening
J. Med. Chem. V. 58 8671 2015
PubMed-ID: 26477515  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01289

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST14
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Strain: 301-5473

 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  (5, 18)

Asymmetric Unit (5, 18)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2OCS2Mod. Amino AcidCYSTEINESULFONIC ACID
3OH2Ligand/IonHYDROXIDE ION
4RHU4Ligand/Ion4-METHYL-5-(TRIFLUOROMETHYL)-1,2,4-TRIAZOLE-3-THIOL
5ZN6Ligand/IonZINC ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2OCS1Mod. Amino AcidCYSTEINESULFONIC ACID
3OH-1Ligand/IonHYDROXIDE ION
4RHU2Ligand/Ion4-METHYL-5-(TRIFLUOROMETHYL)-1,2,4-TRIAZOLE-3-THIOL
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2OCS1Mod. Amino AcidCYSTEINESULFONIC ACID
3OH-1Ligand/IonHYDROXIDE ION
4RHU2Ligand/Ion4-METHYL-5-(TRIFLUOROMETHYL)-1,2,4-TRIAZOLE-3-THIOL
5ZN-1Ligand/IonZINC ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:116 , HIS A:118 , HIS A:196 , RHU A:1298 , OH A:1302 , HOH A:2001BINDING SITE FOR RESIDUE ZN A1001
02AC2SOFTWAREASP A:120 , ARG A:121 , OCS A:221 , HIS A:263 , RHU A:1298 , OH A:1302BINDING SITE FOR RESIDUE ZN A1002
03AC3SOFTWAREHIS A:170 , HIS A:285 , RHU A:1299 , CL A:1300 , CL A:1301BINDING SITE FOR RESIDUE ZN A1003
04AC4SOFTWAREHIS B:116 , HIS B:118 , HIS B:196 , RHU B:1298 , OH B:1302 , HOH B:2001BINDING SITE FOR RESIDUE ZN B1001
05AC5SOFTWAREASP B:120 , ARG B:121 , OCS B:221 , HIS B:263 , RHU B:1298 , OH B:1302BINDING SITE FOR RESIDUE ZN B1002
06AC6SOFTWAREHIS B:170 , HIS B:285 , RHU B:1299 , CL B:1300 , CL B:1301BINDING SITE FOR RESIDUE ZN B1003
07AC7SOFTWARETYR B:137 , HIS B:170 , THR B:229 , HIS B:285 , ASN B:288 , ALA B:292 , ZN B:1003 , CL B:1300 , CL B:1301 , HOH B:2055 , HOH B:2126 , HOH B:2168 , HOH B:2259BINDING SITE FOR RESIDUE RHU B1299
08AC8SOFTWAREALA A:135 , HIS A:170 , HIS A:285 , ASN A:288 , ZN A:1003 , RHU A:1299 , HOH A:2333BINDING SITE FOR RESIDUE CL A1300
09AC9SOFTWAREHIS B:170 , HIS B:285 , ASN B:288 , ZN B:1003 , RHU B:1299 , CL B:1301BINDING SITE FOR RESIDUE CL B1300
10BC1SOFTWAREHIS B:170 , HIS B:285 , ZN B:1003 , RHU B:1299 , CL B:1300BINDING SITE FOR RESIDUE CL B1301
11BC2SOFTWARETRP A:87 , HIS A:116 , HIS A:118 , ASP A:120 , HIS A:196 , OCS A:221 , HIS A:263 , ZN A:1001 , ZN A:1002 , HOH A:2001 , HOH A:2150 , HOH A:2347BINDING SITE FOR RESIDUES RHU A1298 AND OH A1302
12BC3SOFTWARETRP A:87 , HIS A:116 , HIS A:118 , ASP A:120 , HIS A:196 , OCS A:221 , HIS A:263 , ZN A:1001 , ZN A:1002 , HOH A:2001 , HOH A:2150 , HOH A:2347BINDING SITE FOR RESIDUES RHU A1298 AND OH A1302
13BC4SOFTWAREALA A:135 , TYR A:137 , HIS A:170 , THR A:229 , HIS A:285 , ASN A:288 , ALA A:292 , ZN A:1003 , CL A:1300 , HOH A:2082 , HOH A:2142BINDING SITE FOR RESIDUES RHU A1299 AND CL A1301
14BC5SOFTWAREALA A:135 , TYR A:137 , HIS A:170 , THR A:229 , HIS A:285 , ASN A:288 , ALA A:292 , ZN A:1003 , CL A:1300 , HOH A:2082 , HOH A:2142BINDING SITE FOR RESIDUES RHU A1299 AND CL A1301
15BC6SOFTWAREPHE B:61 , TRP B:87 , HIS B:116 , HIS B:118 , ASP B:120 , HIS B:196 , OCS B:221 , HIS B:263 , ZN B:1001 , ZN B:1002 , HOH B:2001 , HOH B:2136 , HOH B:2140 , HOH B:2327BINDING SITE FOR RESIDUES RHU B1298 AND OH B1302
16BC7SOFTWAREPHE B:61 , TRP B:87 , HIS B:116 , HIS B:118 , ASP B:120 , HIS B:196 , OCS B:221 , HIS B:263 , ZN B:1001 , ZN B:1002 , HOH B:2001 , HOH B:2136 , HOH B:2140 , HOH B:2327BINDING SITE FOR RESIDUES RHU B1298 AND OH B1302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ACW)

(-) 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:233
                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh....eeeeeee..eeeeeeeeee..eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeehhhhhhhhhhhh.....ee........eeeee..eeeee..........eeee....eeeeehhh.................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5acw A  29 GEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGcAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRS 297
                                    38      ||49        59    ||  70        80        90       100|    ||112       122       133       143      |167       177       187       197       210||     223       233       243       253       263 ||    284       294   
                                           45|               64|                               100|  107|                   131|              150|                                     205| ||     |                                         265|                    
                                            47                66                                102   109                    133               165                                      209 ||     |                                          277                    
                                                                                                                                                                                          211|     |                                                                 
                                                                                                                                                                                           215     |                                                                 
                                                                                                                                                                                                 221-OCS                                                             


Chain B from PDB  Type:PROTEIN  Length:233
                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh....eeeeeee..eeeeeeeeee..eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeehhhhhhhhhhhh.....ee.........eeee..eeee...........eeee....eeeeehhh.................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5acw B  29 GEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGcAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRS 297
                                    38      ||49        59    ||  70        80        90       100|    ||112       122       133       143      |167       177       187       197       210||     223       233       243       253       263 ||    284       294   
                                           45|               64|                               100|  107|                   131|              150|                                     205| ||     |                                         265|                    
                                            47                66                                102   109                    133               165                                      209 ||     |                                          277                    
                                                                                                                                                                                          211|     |                                                                 
                                                                                                                                                                                           215     |                                                                 
                                                                                                                                                                                                 221-OCS
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

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        Q9K2N0_PSEAI | Q9K2N0: 5k48 5n4s 5n4t 5nhz 5ni0
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        Q9K2N0_PSEAI | Q9K2N0: 1ko2 1ko3 4bz3 4c1d 4c1e 4nq2 4pvo 4pvt 4ua4 5acu 5acv 5acx 5fqc 5lca 5lcf 5lch 5le1 5lm6

(-) Related Entries Specified in the PDB File

5acu VIM-2-NAT, DISCOVERY OF NOVEL INHIBITOR SCAFFOLDS AGAINST THE METALLO-BETA-LACTAMASE VIM-2 BY SPR BASED FRAGMENT SCREENING
5acv VIM-2-NAT, DISCOVERY OF NOVEL INHIBITOR SCAFFOLDS AGAINST THE METALLO-BETA-LACTAMASE VIM-2 BY SPR BASED FRAGMENT SCREENING
5acx VIM-2-2, DISCOVERY OF NOVEL INHIBITOR SCAFFOLDS AGAINST THE METALLO-BETA-LACTAMASE VIM-2 BY SPR BASED FRAGMENT SCREENING