SMTL ID : 6ohp.3 (3 other biounits)

Structure of compound 1 (halopemide) bound human Phospholipase D2 catalytic domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

1 x MJV: N-{2-[4-(5-chloro-2-oxo-2,3-dihydro-1H-benzimidazol-1-yl)piperidin-1-yl]ethyl}-4-fluorobenzamide(Non-covalent)

MJV.1: 21 residues within 4Å: Chain A: W.71, W.72, L.116, G.117, I.118, L.145, A.147, H.149, R.171, L.221, D.225, W.226, W.247, Q.349, F.350, G.393, F.394, Y.461, N.480, R.484, D.491 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.71, A:W.71, A:W.72, A:I.118, A:D.225, A:W.226, A:F.350, A:F.394 Hydrogen bonds: A:R.171, A:R.171, A:Q.349, A:N.480 Water bridges: A:G.393 Halogen bonds: A:L.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Metrick, C.M. et al., Human PLD structures enable drug design and characterization of isoenzyme selectivity. Nat.Chem.Biol. (2020)

Release Date

2020-02-19

Peptides

Phospholipase D2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Phospholipase D2

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