Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  DISCOVERY OF A POTENT AND SELECTIVE MPGES-1 INHIBITOR FOR THE TREATMENT OF PAIN
 
Authors :  M. J. Fisher, M. A. Schiffler, S. L. Kuklish, S. Antonysamy, J. G. Luz
Date :  29 May 15  (Deposition) - 13 Apr 16  (Release) - 13 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Mpges-1, Enzyme, Integral Membrane Protein, Targetname, Isomerase- Isomerase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. A. Schiffler, S. Antonysamy, S. N. Bhattachar, K. M. Campanale, S. Chandrasekhar, B. Condon, P. V. Desai, M. J. Fisher, C. Groshong, A. Harvey, M. J. Hickey, N. E. Hughes, S. A. Jones, E. J. Kim, S. L. Kuklish, J. G. Luz, B. H. Norman, R. E. Rathmell, J. R. Rizzo, T. W. Seng, S. J. Thibodeaux, T. A. Woods, J. S. York, X. P. Yu
Discovery And Characterization Of 2-Acylaminoimidazole Microsomal Prostaglandin E Synthase-1 Inhibitors.
J. Med. Chem. V. 59 194 2016
PubMed-ID: 26653180  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01249

(-) Compounds

Molecule 1 - PROSTAGLANDIN E SYNTHASE
    ChainsA
    EC Number5.3.99.3
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Taxid7108
    GenePTGES, MGST1L1, MPGES1, PGES, PIG12
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMICROSOMAL GLUTATHIONE S-TRANSFERASE 1-LIKE 1,MGST1-L1, MICROSOMAL PROSTAGLANDIN E SYNTHASE 1,MPGES-1,P53-INDUCED GENE 12 PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (3x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric Unit (5, 6)
No.NameCountTypeFull Name
11KA1Ligand/Ion(2-HYDROXYETHOXY)ACETALDEHYDE
24UL1Ligand/Ion2-(DIFLUOROMETHYL)-5-{[(2-METHYLPROPANOYL)AMINO]METHYL}-N-{5-METHYL-4-[4-(TRIFLUOROMETHYL)PHENYL]-1H-IMIDAZOL-2-YL}PYRIDINE-3-CARBOXAMIDE
3BOG2Ligand/IonB-OCTYLGLUCOSIDE
4GSH1Ligand/IonGLUTATHIONE
5PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (5, 18)
No.NameCountTypeFull Name
11KA3Ligand/Ion(2-HYDROXYETHOXY)ACETALDEHYDE
24UL3Ligand/Ion2-(DIFLUOROMETHYL)-5-{[(2-METHYLPROPANOYL)AMINO]METHYL}-N-{5-METHYL-4-[4-(TRIFLUOROMETHYL)PHENYL]-1H-IMIDAZOL-2-YL}PYRIDINE-3-CARBOXAMIDE
3BOG6Ligand/IonB-OCTYLGLUCOSIDE
4GSH3Ligand/IonGLUTATHIONE
5PG43Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:35 , ASP A:49 , ARG A:52 , HIS A:53 , ALA A:123 , PRO A:124 , SER A:127 , LEU A:132 , GSH A:202 , HOH A:316 , HOH A:358binding site for residue 4UL A 201
2AC2SOFTWAREALA A:31 , THR A:34 , ARG A:38 , LEU A:69 , ARG A:70 , ASN A:74 , GLU A:77 , HIS A:113 , TYR A:117 , ARG A:126 , SER A:127 , TYR A:130 , 4UL A:201 , HOH A:303 , HOH A:309 , HOH A:314 , HOH A:333 , HOH A:355binding site for residue GSH A 202
3AC3SOFTWAREGLY A:54 , GLN A:57 , SER A:139 , GLN A:143 , TRP A:146 , PG4 A:205 , HOH A:347binding site for residue BOG A 203
4AC4SOFTWARELEU A:118 , LYS A:120binding site for residue BOG A 204
5AC5SOFTWAREMET A:101 , VAL A:105 , BOG A:203binding site for residue PG4 A 205

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:123 -Pro A:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BQI)

(-) 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:148
                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bqi A   5 SLVMSSPALPAFLLCSTLLVIKMYVVAIITGQVRLRKKAFANPEDALRHGGPQYCRSDPDVERCLRAHRNDMETIYPFLFLGFVYSFLGPNPFVAWMHFLVFLVGRVAHTVAYLGKLRAPIRSVTYTLAQLPCASMALQILWEAARHL 152
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144        

   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    1KA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    4UL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    BOG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GSH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:123 - Pro A:124   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5bqi
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PTGES_HUMAN | O14684
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  5.3.99.3
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  PTGES_HUMAN | O14684
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PTGES_HUMAN | O146843dww 4al0 4al1 4bpm 4wab 4yk5 4yl0 4yl1 4yl3 5bqg 5bqh 5k0i 5t36 5t37 5tl9

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5BQI)