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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 :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Spla2, Secreted Phospholipase A2, 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 - PHOSPHOLIPASE A2, MEMBRANE ASSOCIATED
    Chains: A, B
    EC Number: 3.1.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Plasmid: EXPRESSION_SYSTEM_VECTOR: PET24A
    Synonym: 3SECRETED PHOSPHOLIPASE A2 TYPE IIA, GIIC SPLA2, GROUP IIA PHOSPHOLIPASE A2, NON-PANCREATIC SECRETORY PHOSPHOLIPASE A2, NPS-PLA2, PHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE 2A

 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  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2FMT2Ligand/IonFORMIC ACID
3X282Ligand/Ion3-(5'-BENZYL-2'-CARBAMOYLBIPHENYL-3-YL)PROPANOIC ACID
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2FMT1Ligand/IonFORMIC ACID
3X281Ligand/Ion3-(5'-BENZYL-2'-CARBAMOYLBIPHENYL-3-YL)PROPANOIC ACID
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2FMT1Ligand/IonFORMIC ACID
3X281Ligand/Ion3-(5'-BENZYL-2'-CARBAMOYLBIPHENYL-3-YL)PROPANOIC ACID

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:27 , GLY A:29 , GLY A:31 , ASP A:48 , X28 A:1129BINDING SITE FOR RESIDUE CA A 198
2AC2SOFTWAREPHE A:23 , GLY A:25 , TYR A:112 , ASN A:114 , HOH A:2028BINDING SITE FOR RESIDUE CA A 199
3AC3SOFTWAREHIS B:27 , GLY B:29 , GLY B:31 , ASP B:48 , X28 B:1126BINDING SITE FOR RESIDUE CA B 198
4AC4SOFTWAREPHE B:23 , GLY B:25 , TYR B:112 , HOH B:2024BINDING SITE FOR RESIDUE CA B 199
5AC5SOFTWAREHIS A:6 , ARG A:7 , HOH A:2005BINDING SITE FOR RESIDUE FMT A1128
6AC6SOFTWARESER A:76 , HIS B:6 , ARG B:7 , LYS B:10BINDING SITE FOR RESIDUE FMT B1125
7AC7SOFTWARELEU A:2 , PHE A:5 , HIS A:6 , HIS A:27 , CYS A:28 , GLY A:29 , VAL A:30 , GLY A:31 , HIS A:47 , ASP A:48 , TYR A:51 , CA A:198BINDING SITE FOR RESIDUE X28 A1129
8AC8SOFTWARELEU B:2 , PHE B:5 , HIS B:6 , HIS B:27 , CYS B:28 , GLY B:29 , VAL B:30 , GLY B:31 , CYS B:44 , HIS B:47 , ASP B:48 , CA B:198 , HOH B:2066BINDING SITE FOR RESIDUE X28 B1126

(-) SS Bonds  (14, 14)

Asymmetric Unit
No.Residues
1A:26 -A:117
2A:28 -A:44
3A:43 -A:97
4A:49 -A:124
5A:50 -A:90
6A:59 -A:83
7A:77 -A:88
8B:26 -B:117
9B:28 -B:44
10B:43 -B:97
11B:49 -B:124
12B:50 -B:90
13B:59 -B:83
14B:77 -B:88

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5G3N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5G3N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5G3N)

(-) Exons   (0, 0)

(no "Exon" information available for 5G3N)

(-) 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:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhhhhhhh.........eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5g3n A   1 ALVNFHRMIKLTTGKEAALSYGFYGCHCGVGGRGSPKDATDRCCVTHDCCYKRLEKRGCGTKFLSYKFSNSGSRISCAKQDSCRSQLCECDKAAATCFARNKTTYNKKYQYYSNKHCRGSTPRCGHH 127
                                    10        20        30        40        50        60        70        80        90       100       110       120       


Chain B from PDB  Type:PROTEIN  Length:125
                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhhhhhhhh.........eeee..eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 5g3n B   1 ALVNFHRMIKLTTGKEAALSYGFYGCHCGVGGRGSPKDATDRCCVTHDCCYKRLEKRGCGTKFLSYKFSNSGSRISCAKQDSCRSQLCECDKAAATCFARNKTTYNKKYQYYSNKHCRGSTPRCG 125
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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 5G3N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5G3N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5G3N)

(-) Gene Ontology  (29, 29)

Asymmetric Unit(hide GO term definitions)

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        PA2GA_HUMAN | P14555: 1ayp 1bbc 1db4 1db5 1dcy 1j1a 1kqu 1kvo 1n28 1n29 1pod 1poe 2gny 3u8b 3u8d 3u8h 3u8i

(-) Related Entries Specified in the PDB File

5g3m DISCOVERY OF A NOVEL SECRETED PHOSPHOLIPASE A2 (SPLA2) INHIBITOR.