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

Structure of compound 4 bound human Phospholipase D2 catalytic domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

monomer

Ligands

1 x MKA: 4-fluoro-N-{(2S)-1-[4-(2-oxo-2,3-dihydro-1H-benzimidazol-1-yl)piperidin-1-yl]propan-2-yl}benzamide(Covalent)

MKA.1: 18 residues within 4Å: Chain A: W.71, W.72, G.117, I.118, H.149, R.171, L.221, D.225, W.226, W.247, Q.349, F.350, G.393, F.394, Y.461, N.480, D.491 Ligands: SO4.7 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.71, A:W.71, A:W.72, A:I.118, A:L.221, A:D.225, A:W.226, A:W.226, A:W.247, A:F.394 Hydrogen bonds: A:R.171, A:R.171, A:N.480 Water bridges: A:D.491

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: W.380, C.381, N.509 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.381, A:N.509 SO4.3: 5 residues within 4Å: Chain A: H.139, P.140, D.141, Q.142, T.276 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.141, A:Q.142, A:T.276 Salt bridges: A:H.139 SO4.4: 2 residues within 4Å: Chain A: G.121, R.138 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.121, A:G.121 Salt bridges: A:R.138 SO4.5: 4 residues within 4Å: Chain A: R.338, Q.341, R.371, W.380 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.341 Salt bridges: A:R.338, A:R.371 SO4.6: 4 residues within 4Å: Chain A: K.429, T.434, W.436, R.437 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.436 Salt bridges: A:K.429, A:R.437 SO4.7: 3 residues within 4Å: Chain A: F.394, R.484 Ligands: MKA.1 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.484 SO4.8: 3 residues within 4Å: Chain A: H.28, R.29, P.36 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.29 Salt bridges: A:H.28 SO4.9: 5 residues within 4Å: Chain A: R.178, L.179, T.180, G.449, E.450 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.179, A:T.180, A:T.180, A:E.450 SO4.10: 6 residues within 4Å: Chain A: F.211, L.214, G.215, F.233, D.235, R.239 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.215, A:F.233 Salt bridges: A:R.239 SO4.11: 5 residues within 4Å: Chain A: W.436, I.442, H.612, F.613, L.615 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.442, A:Q.554, A:F.613, A:F.613 Salt bridges: A:H.612 SO4.12: 5 residues within 4Å: Chain A: K.124, R.138, K.277, K.279, Y.280 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.138, A:Y.280 Salt bridges: A:K.110, A:K.124, A:R.138, A:K.277, A:K.279 SO4.13: 8 residues within 4Å: Chain A: E.76, V.77, Y.78, R.81, Y.169, F.212, L.214, D.217 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.78, A:L.214, A:D.217 Water bridges: A:D.217 Salt bridges: A:R.81

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
A

Phospholipase D2

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