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(-) Description

Title :  COMPLEX OF HUMAN HEMATOPOIETIC PROSTAGANDIN D2 SYNTHASE (HH-PGDS) IN COMPLEX WITH AN ACTIVE SITE INHIBITOR.
 
Authors :  F. Edfeldt, J. Evenas, M. Lepisto, A. Ward, J. Petersen, L. Wissler, M. R U. Sivars, K. Svensson, M. Perry, I. Feierberg, X. Zhou, T. Hansson, F.
Date :  17 Feb 15  (Deposition) - 03 Jun 15  (Release) - 10 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Transferase, Prostaglandin D2 Synthase, Pgds Inhibitors, Indole, Focused Screening, Hit Validation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Edfeldt, J. Even, M. Lepisto, A. Ward, J. Petersen, L. Wissler, M. Rohman, U. Sivars, K. Svensson, M. Perry, I. Feierberg, X. H. Zhou, T. Hansson, F. Narjes
Identification Of Indole Inhibitors Of Human Hematopoietic Prostaglandin D2 Synthase (Hh-Pgds).
Bioorg. Med. Chem. Lett. V. 25 2496 2015
PubMed-ID: 25978964  |  Reference-DOI: 10.1016/J.BMCL.2015.04.065

(-) Compounds

Molecule 1 - HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE
    Chains: A, C, B, D
    EC Number: 5.3.99.2, 2.5.1.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: H-PGDS, GST CLASS-SIGMA, GLUTATHIONE S-TRANSFERASE, GLUTATH IONE-DEPENDENT PGD SYNTHASE, GLUTATHIONE-REQUIRING PROSTAGLANDIN D SYNTHASE, PROSTAGLANDIN-H2 D-ISOMERASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1CWC4Ligand/Ion4-(DIMETHYLAMINO)-N-[5-(1H-INDOL-4-YL)PYRIDIN-3-YL]BUTANAMIDE
2GSH4Ligand/IonGLUTATHIONE
3MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CWC2Ligand/Ion4-(DIMETHYLAMINO)-N-[5-(1H-INDOL-4-YL)PYRIDIN-3-YL]BUTANAMIDE
2GSH2Ligand/IonGLUTATHIONE
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CWC2Ligand/Ion4-(DIMETHYLAMINO)-N-[5-(1H-INDOL-4-YL)PYRIDIN-3-YL]BUTANAMIDE
2GSH2Ligand/IonGLUTATHIONE
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE C:9 , MET C:11 , GLY C:13 , ARG C:14 , ASP C:96 , MET C:99 , TRP C:104 , TYR C:152 , GSH C:1201BINDING SITE FOR RESIDUE CWC C1200
02AC2SOFTWAREPHE D:9 , MET D:11 , GLY D:13 , ARG D:14 , GLN D:36 , ASP D:96 , MET D:99 , TRP D:104 , TYR D:152 , LEU D:199 , GSH D:1202 , HOH D:2006 , HOH D:2032BINDING SITE FOR RESIDUE CWC D1200
03AC3SOFTWAREMET A:11 , GLY A:13 , ARG A:14 , ASP A:96 , MET A:99 , TRP A:104 , TYR A:152 , GSH A:1201BINDING SITE FOR RESIDUE CWC A1200
04AC4SOFTWARETYR B:8 , MET B:11 , GLY B:13 , ARG B:14 , GLN B:36 , ASP B:96 , MET B:99 , TRP B:104 , TYR B:152 , GSH B:1202 , HOH B:2012BINDING SITE FOR RESIDUE CWC B1200
05AC5SOFTWAREHOH C:2043 , HOH C:2045 , HOH C:2049 , HOH D:2029 , HOH D:2030 , HOH D:2031BINDING SITE FOR RESIDUE MG D1201
06AC6SOFTWAREHOH A:2044 , HOH A:2045 , HOH A:2049 , HOH B:2048 , HOH B:2051 , HOH B:2052BINDING SITE FOR RESIDUE MG B1201
07AC7SOFTWAREASP C:97 , TYR D:8 , ARG D:14 , TRP D:39 , LYS D:50 , ILE D:51 , GLN D:63 , SER D:64 , CWC D:1200 , HOH D:2022BINDING SITE FOR RESIDUE GSH D1202
08AC8SOFTWARETYR C:8 , ARG C:14 , TRP C:39 , LYS C:43 , LYS C:50 , ILE C:51 , PRO C:52 , GLN C:63 , SER C:64 , CWC C:1200 , HOH C:2009 , HOH C:2027 , HOH C:2048 , ASP D:97BINDING SITE FOR RESIDUE GSH C1201
09AC9SOFTWAREASP A:97 , TYR B:8 , ARG B:14 , TRP B:39 , LYS B:43 , LYS B:50 , ILE B:51 , PRO B:52 , GLN B:63 , SER B:64 , CWC B:1200 , HOH B:2015 , HOH B:2016 , HOH B:2034BINDING SITE FOR RESIDUE GSH B1202
10BC1SOFTWARETYR A:8 , ARG A:14 , TRP A:39 , LYS A:43 , LYS A:50 , ILE A:51 , GLN A:63 , SER A:64 , CWC A:1200 , HOH A:2008 , HOH A:2024 , HOH A:2050 , ASP B:97BINDING SITE FOR RESIDUE GSH A1201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ile A:51 -Pro A:52
2Ile B:51 -Pro B:52
3Ile C:51 -Pro C:52
4Ile D:51 -Pro D:52

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5AIS)

(-) 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:198
                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh....eeeee...hhhhhhhhh......eeee..eeeehhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ais 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
                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh....eeeeehhhhhhhhhh........eeee...eeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ais B   2 PNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGKIPILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSCFPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADFYWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL 199
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191        


Chain C from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhh...eeeeee...hhhhhhhhh......eeee..eeeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ais C   2 PNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGKIPILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSCFPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADFYWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL 199
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191        


Chain D from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhh......eeee..eeeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ais D   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)
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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 5AIS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)

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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 3kxo 3vi5 3vi7 4ec0 4edy 4edz 4ee0 5aiv 5aix

(-) Related Entries Specified in the PDB File

5aiv COMPLEX OF HUMAN HEMATOPOIETIC PROSTAGANDIN D2 SYNTHASE ( HH-PGDS) IN COMPLEX WITH AN ACTIVE SITE INHIBITOR.