SMTL ID : 6ohq.2 (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(Non-covalent)

MKA.1: 17 residues within 4Å: Chain A: W.71, W.72, G.117, I.118, A.147, H.149, R.171, L.221, D.225, W.226, W.247, Q.349, G.393, N.480, R.484, D.491 Ligands: SO4.7 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:W.71, A:W.71, A:W.72, A:I.118, A:A.147, A:L.221, A:D.225, A:W.226, A:W.226, A:W.247 Hydrogen bonds: A:R.171, A:R.171, A:N.480, A:D.491, A:D.491 Water bridges: A:D.225, A:G.393

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: 3 residues within 4Å: Chain A: T.434, W.436, R.437 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.429, A:R.437 SO4.4: 5 residues within 4Å: Chain A: R.178, L.179, T.180, G.449, E.450 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.179, A:T.180, A:E.450 SO4.5: 1 residues within 4Å: Chain A: R.472 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.472 SO4.6: 7 residues within 4Å: Chain A: L.390, R.446, A.561, Y.564, P.572, V.611, H.612 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.572 Salt bridges: A:R.446 SO4.7: 5 residues within 4Å: Chain A: F.394, R.484, V.638, W.639 Ligands: MKA.1 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.484 SO4.8: 3 residues within 4Å: Chain A: I.92, K.95, R.96 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.95 Salt bridges: A:K.95, A:R.96 SO4.9: 5 residues within 4Å: Chain A: Q.26, H.28, R.29, P.35, P.36 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.26, A:R.29 Salt bridges: A:H.28 SO4.10: 6 residues within 4Å: Chain A: W.436, I.440, S.441, I.442, Q.554, H.612 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.442, A:Q.554, A:Q.554 Salt bridges: A:H.612 SO4.11: 3 residues within 4Å: Chain A: Q.341, R.371, K.374 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.341 Salt bridges: A:R.371, A:K.374 SO4.12: 4 residues within 4Å: Chain A: K.110, K.124, R.138, Y.280 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.280 Salt bridges: A:K.110, A:K.124, A:R.138 SO4.13: 3 residues within 4Å: Chain A: M.432, G.433, T.434 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.434 Water bridges: A:T.434

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
B

Phospholipase D2

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