SMTL ID : 6g5j.1 (1 other biounit)

Secreted phospholipase A2 type X in complex with ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: F.68, G.70, G.72, D.89 Ligands: EM8.2 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:F.68, A:G.70, A:G.72, A:D.89, A:D.89

2 x EM8: (3~{R})-3-[3-[2-aminocarbonyl-6-(trifluoromethyloxy)indol-1-yl]phenyl]butanoic acid(Non-covalent)

EM8.2: 18 residues within 4Å: Chain A: I.44, L.47, P.59, I.60, Y.62, M.63, F.68, C.69, G.70, L.71, G.72, C.85, H.88, D.89, Y.92, K.103, I.136 Ligands: CA.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.44, A:L.47, A:Y.62, A:Y.92, A:K.103, A:I.136 Hydrogen bonds: A:G.70, A:G.72, A:H.88, A:D.89, A:D.89 EM8.3: 6 residues within 4Å: Chain A: R.57, T.58, I.60, A.61, Y.145, F.151 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.58, A:I.60, A:A.61, A:Y.145 Water bridges: A:T.58, A:T.58, A:T.58 Salt bridges: A:R.57

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 5 residues within 4Å: Chain A: R.106, S.108, P.120, E.122, Q.126 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.108 Water bridges: A:S.108

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 10 residues within 4Å: Chain A: K.64, Y.65, G.66, C.67, F.68, C.69, G.70, L.71, G.72, G.73 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Giordanetto, F. et al., Design of Selective sPLA2-X Inhibitor (-)-2-{2-[Carbamoyl-6-(trifluoromethoxy)-1H-indol-1-yl]pyridine-2-yl}propanoic Acid. ACS Med Chem Lett (2018)

Release Date

2018-09-05

Peptides

Group 10 secretory phospholipase A2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Group 10 secretory phospholipase A2

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