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(-) Description

Title :  AN ORALLY ACTIVE INHIBITOR BOUND AT THE ACTIVE SITE OF HPGDS
 
Authors :  J. R. Kiefer, J. E. Day, A. Thorarensen
Date :  03 Dec 09  (Deposition) - 01 Sep 10  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  H-Pgds, Pgds, Hpgds, Fatty Acid Biosynthesis, Isomerase, Lipid Synthesis, Prostaglandin Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. P. Carron, J. I. Trujillo, K. L. Olson, W. Huang, B. C. Hamper, T. Dice B. E. Neal, M. J. Pelc, J. Day, D. C. Rohrer, J. R. Kiefer, J. B. Moon, B. A. Schweitzer, T. D. Blake, S. R. Turner, R. Woerndle, B. L. Case, C. P. Bono, V. M. Dilworth, C. L. Funckes-Shippy, B. L. Hood, G. M. Jerome, C. M. Kornmeier, M. R. Radabaugh, M. L. Williams, M. S. Davies, C. D. Wegner, D. J. Welsch, W. M. Abraham, C. J. Warren, M. E. Dowty, F. Hua, A. Zutshi, J. Z. Yang, A. Thorarensen
Discovery Of An Oral Potent Selective Inhibitor Of Hematopoietic Prostaglandin D Synthase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLUTATHIONE-REQUIRING PROSTAGLANDIN D SYNTHASE
    Chains: A, B
    EC Number: 5.3.99.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PTGDS2, PGDS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GLUTATHIONE-DEPENDENT PGD SYNTHETASE, PROSTAGLANDIN-H2 D- ISOMERASE, HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE, H-PGDS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1GSH2Ligand/IonGLUTATHIONE
2KXO2Ligand/Ion6-(3-FLUOROPHENYL)-N-[1-(2,2,2-TRIFLUOROETHYL)PIPERIDIN-4-YL]PYRIDINE-3-CARBOXAMIDE
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:8 , ARG A:14 , TRP A:39 , LYS A:43 , LYS A:50 , ILE A:51 , GLN A:63 , SER A:64 , KXO A:202 , HOH A:3001 , HOH A:3117 , HOH A:3125 , HOH A:3137 , ASP B:97BINDING SITE FOR RESIDUE GSH A 201
2AC2SOFTWAREPHE A:9 , MET A:11 , GLY A:13 , ARG A:14 , GLN A:36 , TRP A:39 , MET A:99 , TRP A:104 , TYR A:152 , CYS A:156 , LEU A:199 , GSH A:201 , HOH A:3111 , HOH A:3113 , HOH A:3137BINDING SITE FOR RESIDUE KXO A 202
3AC3SOFTWAREHOH A:3097 , HOH A:3104 , HOH A:3112 , HOH B:3068 , HOH B:3079 , HOH B:3116BINDING SITE FOR RESIDUE MG B 201
4AC4SOFTWAREASP A:97 , TYR B:8 , ARG B:14 , TRP B:39 , LYS B:43 , LYS B:50 , ILE B:51 , GLN B:63 , SER B:64 , KXO B:203 , HOH B:3010 , HOH B:3050 , HOH B:3124 , HOH B:3126BINDING SITE FOR RESIDUE GSH B 202
5AC5SOFTWAREPHE B:9 , MET B:11 , ARG B:14 , GLN B:36 , MET B:99 , TRP B:104 , TYR B:152 , LEU B:199 , GSH B:202 , HOH B:3028 , HOH B:3121BINDING SITE FOR RESIDUE KXO B 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KXO)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile A:51 -Pro A:52
2Ile B:51 -Pro B:52

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KXO)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GST_NTERPS50404 Soluble glutathione S-transferase N-terminal domain profile.HPGDS_HUMAN2-79
 		  2A:2-79
B:2-79
2GST_CTERPS50405 Soluble glutathione S-transferase C-terminal domain profile.HPGDS_HUMAN81-199
 		  2A:81-199
B:81-199

(-) Exons   (5, 10)

Asymmetric/Biological Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002952561aENSE00001428701chr4:95264027-9526394682HPGDS_HUMAN-00--
1.2aENST000002952562aENSE00002147371chr4:95255789-95255648142HPGDS_HUMAN1-45452A:2-45
B:2-45		44
44
1.3ENST000002952563ENSE00001238639chr4:95239116-9523902493HPGDS_HUMAN45-76322A:45-76
B:45-76		32
32
1.4ENST000002952564ENSE00001071670chr4:95229894-95229785110HPGDS_HUMAN76-112372A:76-112
B:76-112		37
37
1.6ENST000002952566ENSE00001071668chr4:95223395-9522329799HPGDS_HUMAN113-145332A:113-145
B:113-145		33
33
1.7ENST000002952567ENSE00001302624chr4:95220795-952196861110HPGDS_HUMAN146-199542A:146-199
B:146-199		54
54

(-) 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:198
 aligned with HPGDS_HUMAN | O60760 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:198
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191        
          HPGDS_HUMAN     2 PNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGKIPILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSCFPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADFYWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL 199
               SCOP domains d3kxoa1 A:2-75 automated matches                                          d3kxoa2 A:76-199 automated matches                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhh...eeeeeehhhhhhhhhhhh......eeee..eeeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE GST_NTER  PDB: A:2-79 UniProt: 2-79                                           -GST_CTER  PDB: A:81-199 UniProt: 81-199                                                                                 PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:2-45 UniProt: 1-45        ------------------------------Exon 1.4  PDB: A:76-112              Exon 1.6  PDB: A:113-145         Exon 1.7  PDB: A:146-199 UniProt: 146-199              Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.3  PDB: A:45-76          --------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3kxo A   2 PNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGKIPILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSCFPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADFYWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL 199
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191        


Chain B from PDB  Type:PROTEIN  Length:198
 aligned with HPGDS_HUMAN | O60760 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:198
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191        
          HPGDS_HUMAN     2 PNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGKIPILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSCFPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADFYWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL 199
               SCOP domains d3kxob1 B:2-75 automated matches                                          d3kxob2 B:76-199 automated matches                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --GST_N-3kxoB03 B:4-73                                                  -------GST_C-3kxoB01 B:81-185                                                                                   -------------- Pfam domains (1)
           Pfam domains (2) --GST_N-3kxoB04 B:4-73                                                  -------GST_C-3kxoB02 B:81-185                                                                                   -------------- Pfam domains (2)
         Sec.struct. author ..eeeeee.....hhhhhhhhhhh....eeeeehhhhhhhhhh........eeee..eeeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE GST_NTER  PDB: B:2-79 UniProt: 2-79                                           -GST_CTER  PDB: B:81-199 UniProt: 81-199                                                                                 PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: B:2-45 UniProt: 1-45        ------------------------------Exon 1.4  PDB: B:76-112              Exon 1.6  PDB: B:113-145         Exon 1.7  PDB: B:146-199 UniProt: 146-199              Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.3  PDB: B:45-76          --------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3kxo B   2 PNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGKIPILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSCFPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADFYWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL 199
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KXO)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: GST_C (118)
(-)
Family: GST_C (102)
(-)
Clan: Thioredoxin (367)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (HPGDS_HUMAN | O60760)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0004364    glutathione transferase activity    Catalysis of the reaction: R-X + glutathione = H-X + R-S-glutathione. R may be an aliphatic, aromatic or heterocyclic group; X may be a sulfate, nitrile or halide group.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004667    prostaglandin-D synthase activity    Catalysis of the reaction: prostaglandin H(2) = prostaglandin D(2).
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0019371    cyclooxygenase pathway    The chemical reactions and pathways by which prostaglandins are formed from arachidonic acid, and in which prostaglandin-endoperoxide synthase (cyclooxygenase) catalyzes the committed step in the conversion of arachidonic acid to the prostaglandin-endoperoxides PGG2 and PGH2.
    GO:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:1901687    glutathione derivative biosynthetic process    The chemical reactions and pathways resulting in the formation of glutathione derivative.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0007626    locomotory behavior    The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.
    GO:2000255    negative regulation of male germ cell proliferation    Any process that stops, prevents or reduces the frequency, rate or extent of male germ cell proliferation.
    GO:0001516    prostaglandin biosynthetic process    The chemical reactions and pathways resulting in the formation of prostaglandins, any of a group of biologically active metabolites which contain a cyclopentane ring.
    GO:0006693    prostaglandin metabolic process    The chemical reactions and pathways involving prostaglandins, any of a group of biologically active metabolites which contain a cyclopentane ring due to the formation of a bond between two carbons of a fatty acid. They have a wide range of biological activities.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HPGDS_HUMAN | O60760: 1iyh 1iyi 1v40 2cvd 2vcq 2vcw 2vcx 2vcz 2vd0 2vd1 3ee2 3vi5 3vi7 4ec0 4edy 4edz 4ee0 5ais 5aiv 5aix

(-) Related Entries Specified in the PDB File

2cvd HPGDS COMPLEX WITH HQL-79
2vcx HPGDS COMPLEX WITH AN INHIBITOR FRAGMENT