SMTL ID : 8p96.1

TARGET COMPLEX 3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.86 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: H.185, H.187, H.190, H.253, D.284 Ligands: ZN.2, 3PE.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.185, A:H.187, A:H.253, A:D.284 ZN.2: 7 residues within 4Å: Chain A: H.132, D.189, H.190, D.284, H.343 Ligands: ZN.1, 3PE.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.189, A:H.190, A:D.284, A:H.343 ZN.10: 7 residues within 4Å: Chain B: H.185, H.187, H.190, H.253, D.284 Ligands: ZN.11, 3PE.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.185, B:H.187, B:H.253, B:D.284 ZN.11: 6 residues within 4Å: Chain B: D.189, H.190, D.284, H.343 Ligands: ZN.10, 3PE.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.189, B:H.190, B:D.284, B:H.343

2 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.3: 22 residues within 4Å: Chain A: R.82, A.154, P.156, M.160, P.162, H.187, Y.188, D.189, H.253, W.254, K.256, R.257, T.258, D.284, H.321, H.343, L.349 Ligands: ZN.1, ZN.2, DXC.6, DXC.7, DXC.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.188, A:Y.188 Hydrogen bonds: A:Y.188 Salt bridges: A:H.187, A:H.187, A:H.253, A:H.321 3PE.12: 25 residues within 4Å: Chain B: A.154, P.156, M.160, P.162, H.187, Y.188, D.189, H.253, W.254, K.256, R.257, T.258, L.259, D.284, M.317, Q.320, H.321, H.343, L.349 Ligands: DXC.8, DXC.9, ZN.10, ZN.11, DXC.13, DXC.16 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:P.162, B:Y.188, B:K.256, B:K.256, B:L.259 Hydrogen bonds: B:Y.188, B:D.189, B:D.189, B:Q.320 Salt bridges: B:H.187, B:H.187, B:H.187, B:H.253, B:H.321, B:H.343

10 x DXC: (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID(Non-covalent)(Non-functional Binders)

DXC.4: 9 residues within 4Å: Chain A: Y.193, W.218, K.221, C.222 Chain B: I.85, Y.159, M.160 Ligands: DXC.13, DXC.15 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.159, B:Y.159, A:K.221 DXC.5: 4 residues within 4Å: Chain A: M.160 Ligands: DXC.7, DXC.9, DXC.14 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.221 DXC.6: 4 residues within 4Å: Chain A: L.259 Ligands: 3PE.3, DXC.13, DXC.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.259 Hydrogen bonds: A:L.259, A:L.259 DXC.7: 6 residues within 4Å: Chain A: R.82, L.84, I.85, L.259 Ligands: 3PE.3, DXC.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:R.82, A:L.84, A:L.84, A:L.84, A:I.85, A:L.259 Hydrogen bonds: A:R.82 DXC.8: 10 residues within 4Å: Chain A: Y.159 Chain B: Y.188, W.218, R.257, T.258 Ligands: 3PE.3, DXC.9, 3PE.12, DXC.13, DXC.14 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.257 Hydrophobic interactions: A:Y.159, A:Y.159 DXC.9: 5 residues within 4Å: Chain B: T.258, L.259 Ligands: DXC.5, DXC.8, 3PE.12 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.258, B:L.259 DXC.13: 10 residues within 4Å: Chain A: Y.188, W.218, R.257 Chain B: Y.159, M.160 Ligands: DXC.4, DXC.6, DXC.8, 3PE.12, DXC.15 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.159, B:Y.159, B:Y.159 Hydrogen bonds: B:Y.159, A:Y.188 Salt bridges: A:R.257 DXC.14: 8 residues within 4Å: Chain A: Y.159, M.160 Chain B: Y.193, W.218, K.221, C.222 Ligands: DXC.5, DXC.8 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.159, A:Y.159, B:W.218 Water bridges: A:Y.159 Salt bridges: A:K.88 Hydrogen bonds: B:D.217 DXC.15: 4 residues within 4Å: Ligands: DXC.4, DXC.6, DXC.13, DXC.16 No protein-ligand interaction detected (PLIP) DXC.16: 4 residues within 4Å: Chain B: R.82, L.259 Ligands: 3PE.12, DXC.15 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.82, B:L.259

1 x XBE: naphthalene-1,3,7-trisulfonic acid

XBE.17: 10 residues within 4Å: Chain A: S.151, S.152 Chain B: F.150, S.151, S.152, T.171, I.172, D.192, N.194, A.198 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.152, B:S.152, B:I.172, A:S.152, A:S.152, A:S.152 Water bridges: B:K.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chiarugi, S. et al., NAPE-PLD is target of thiazide diuretics. Cell Chem Biol (2025)

Release Date

2024-06-26

Peptides

N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D

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