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(-) Description

Title :  DISCOVERY OF A NOVEL SECRETED PHOSPHOLIPASE A2 (SPLA2) INHIBITOR.
 
Authors :  J. Sandmark, C. Bodin, K. Hallberg
Date :  29 Apr 16  (Deposition) - 14 Sep 16  (Release) - 09 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Spla2, Cardiovascular Disease, Inhibitor, Fragment (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Giordanetto, D. Pettersen, I. Starke, P. Nordberg, M. Dahlstrom, L. Knerr, N. Selmi, B. Rosengren, L. O. Larsson, J. Sandmark, M. Castaldo, N. Dekker, U. Karlsson, E. Hurt-Camejo
Discovery Of Azd2716: A Novel Secreted Phospholipase A2 (Spla2) Inhibitor For The Treatment Of Coronary Artery Disease
Acs Med. Chem. Lett. V. 7 884 2016
PubMed-ID: 27774123  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.6B00188

(-) Compounds

Molecule 1 - GROUP 10 SECRETORY PHOSPHOLIPASE A2
    Chains: A, B
    EC Number: 3.1.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: GOLD
    Fragment: MATURE SPLA2-X, UNP RESIDUES 43-165
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SECRETED PHOSPHOLIPASE A2, GROUP X SECRETORY PHOSPHOLIPASE A SPLA2-X, PHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE 10

 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  (4, 25)

Asymmetric Unit (4, 25)
No.NameCountTypeFull Name
19JH2Ligand/Ion4-BENZYLBENZAMIDE
2CA2Ligand/IonCALCIUM ION
3DMS10Ligand/IonDIMETHYL SULFOXIDE
4PEG11Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (3, 13)
No.NameCountTypeFull Name
19JH1Ligand/Ion4-BENZYLBENZAMIDE
2CA-1Ligand/IonCALCIUM ION
3DMS5Ligand/IonDIMETHYL SULFOXIDE
4PEG7Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (3, 10)
No.NameCountTypeFull Name
19JH1Ligand/Ion4-BENZYLBENZAMIDE
2CA-1Ligand/IonCALCIUM ION
3DMS5Ligand/IonDIMETHYL SULFOXIDE
4PEG4Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:26 , GLY A:28 , GLY A:30 , ASP A:47 , PEG A:1128 , 9JH A:1134BINDING SITE FOR RESIDUE CA A 200
02AC2SOFTWAREPHE B:26 , GLY B:28 , GLY B:30 , ASP B:47 , PEG B:1132 , 9JH B:1133BINDING SITE FOR RESIDUE CA B 200
03AC3SOFTWAREHIS A:44BINDING SITE FOR RESIDUE DMS A1124
04AC4SOFTWARECYS A:76 , GLN A:92 , ALA B:79BINDING SITE FOR RESIDUE DMS A1125
05AC5SOFTWAREPRO A:14 , ARG A:15 , THR A:16 , LEU B:105 , LYS B:106 , DMS B:1126BINDING SITE FOR RESIDUE DMS B1124
06AC6SOFTWAREVAL B:12 , PRO B:14 , LEU B:29 , GLN B:72BINDING SITE FOR RESIDUE DMS A1140
07AC7SOFTWARELYS A:22 , GLY A:24 , CYS A:25 , CYS A:27 , LEU A:29 , PEG A:1131 , HOH A:2009 , HOH A:2015BINDING SITE FOR RESIDUE DMS A1126
08AC8SOFTWARELYS B:22 , GLY B:24 , CYS B:27 , GLY B:28 , LEU B:29 , GLY B:30 , HOH B:2009BINDING SITE FOR RESIDUE DMS B1125
09AC9SOFTWARETHR A:16 , LEU B:105 , LEU B:108 , DMS B:1124BINDING SITE FOR RESIDUE DMS B1126
10BC1SOFTWAREPRO A:78 , ALA A:79 , LEU B:75 , CYS B:76 , GLN B:92BINDING SITE FOR RESIDUE DMS B1127
11BC2SOFTWARELEU A:114 , LEU B:3 , GLU B:4 , ARG B:64 , TRP B:67BINDING SITE FOR RESIDUE DMS B1128
12BC3SOFTWAREVAL A:74 , GLN A:92 , ASN A:96 , HOH A:2038BINDING SITE FOR RESIDUE DMS A1141
13BC4SOFTWARETRP A:67 , GLN A:68 , CYS A:69 , HOH A:2006 , PEG B:1131BINDING SITE FOR RESIDUE PEG A1127
14BC5SOFTWAREGLY A:28 , GLY A:30 , ASP A:47 , LYS A:61 , CA A:200 , PEG A:1133 , 9JH A:1134BINDING SITE FOR RESIDUE PEG A1128
15BC6SOFTWARELEU B:29 , LYS B:61 , ASN B:71 , GLN B:72 , ASN B:96 , HOH B:2005BINDING SITE FOR RESIDUE PEG B1129
16BC7SOFTWAREARG A:64 , SER A:66 , GLU A:80 , GLN B:68 , PEG B:1131BINDING SITE FOR RESIDUE PEG A1129
17BC8SOFTWAREALA A:19BINDING SITE FOR RESIDUE PEG A1130
18BC9SOFTWARETRP B:67 , CYS B:69 , HOH B:2024BINDING SITE FOR RESIDUE PEG B1130
19CC1SOFTWARETYR A:65 , SER A:66 , TRP A:67 , PEG A:1127 , PEG A:1129 , HOH A:2005 , GLN B:34BINDING SITE FOR RESIDUE PEG B1131
20CC2SOFTWARELEU A:29 , GLY A:31 , HIS A:32 , GLN A:100 , GLN A:112 , DMS A:1126BINDING SITE FOR RESIDUE PEG A1131
21CC3SOFTWAREALA A:38 , THR A:101 , GLU A:102 , GLN A:112BINDING SITE FOR RESIDUE PEG A1132
22CC4SOFTWARELEU A:29 , LYS A:61 , GLN A:72 , SER A:73 , ASN A:96 , PEG A:1128BINDING SITE FOR RESIDUE PEG A1133
23CC5SOFTWAREGLY B:28 , GLY B:30 , ASP B:47 , THR B:51 , GLU B:54 , CA B:200BINDING SITE FOR RESIDUE PEG B1132
24CC6SOFTWARELEU A:5 , PRO A:17 , TYR A:20 , MET A:21 , PHE A:26 , CYS A:27 , GLY A:28 , CYS A:43 , HIS A:46 , ASP A:47 , ILE A:94 , CA A:200 , PEG A:1128BINDING SITE FOR RESIDUE 9JH A1134
25CC7SOFTWAREPRO B:17 , TYR B:20 , PHE B:26 , CYS B:27 , GLY B:28 , CYS B:43 , HIS B:46 , ASP B:47 , ILE B:94 , CA B:200BINDING SITE FOR RESIDUE 9JH B1133

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:11 -A:69
2A:25 -A:115
3A:27 -A:43
4A:42 -A:97
5A:48 -A:122
6A:49 -A:90
7A:58 -A:83
8A:76 -A:88
9B:11 -B:69
10B:25 -B:115
11B:27 -B:43
12B:42 -B:97
13B:48 -B:122
14B:49 -B:90
15B:58 -B:83
16B:76 -B:88

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:77 -Pro A:78
2Gly B:13 -Pro B:14
3Gly B:77 -Pro B:78

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5G3M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5G3M)

(-) Exons   (0, 0)

(no "Exon" information available for 5G3M)

(-) 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:123
                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhh...............hhhhhhhhhhhhhhhhhhhh..........eee....eee....hhhhhhhhhhhhhhhhhhhh...hhhh...hhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 5g3m A   1 GILELAGTVGCVGPRTPIAYMKYGCFCGLGGHGQPRDAIDWCCHGHDCCYTRAEEAGCSPKTERYSWQCVNQSVLCGPAENKCQELLCKCDQEIANCLAQTEYNLKYLFYPQFLCEPDSPKCD 123
                                    10        20        30        40        50        60        70        80        90       100       110       120   


Chain B from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhh...............hhhhhhhhhhhhhhhhhhhh..........eeee..eeee....hhhhhhhhhhhhhhhhhhh....hhhh...hhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 5g3m B   1 GILELAGTVGCVGPRTPIAYMKYGCFCGLGGHGQPRDAIDWCCHGHDCCYTRAEEAGCSPKTERYSWQCVNQSVLCGPAENKCQELLCKCDQEIANCLAQTEYNLKYLFYPQFLCEPDSPKCD 123
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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 5G3M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5G3M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5G3M)

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)

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5g3n DISCOVERY OF A NOVEL SECRETED PHOSPHOLIPASE A2 (SPLA2) INHIBITOR.