SMTL ID : 6tw6.3 (2 other biounits)

Plasmodium vivax N-myristoyltransferase with bound indazole inhibitor IMP-923

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x NHW: 2-oxopentadecyl-CoA(Non-covalent)

NHW.1: 34 residues within 4Å: Chain A: Y.6, K.7, F.8, W.9, N.72, Y.73, V.74, V.138, N.139, F.140, L.141, C.142, V.143, R.148, S.149, K.150, R.151, L.152, A.153, P.154, I.157, T.161, I.164, N.165, W.170, Q.171, A.172, Y.174, T.175, A.176, L.180, Y.371 Ligands: NZE.2, MG.3 37 PLIP interactions: 37 interactions with chain A Hydrophobic interactions: A:W.9, A:W.9, A:Y.73, A:V.74, A:L.141, A:L.141, A:L.141, A:V.143, A:A.153, A:I.157, A:I.164, A:I.164, A:A.172, A:Y.174, A:Y.174, A:Y.371 Hydrogen bonds: A:Y.6, A:K.7, A:F.8, A:W.9, A:F.140, A:L.141, A:L.141, A:V.143, A:R.148, A:R.148, A:S.149, A:R.151, A:L.152, A:A.153 Water bridges: A:S.149, A:R.151, A:R.151, A:R.151, A:R.151 Salt bridges: A:R.151, A:R.151

1 x NZE: [(5-{4-fluoro-2-[2-(1H-imidazol-1-yl)ethoxy]phenyl}-1H-indazol-3-yl)methyl]dimethylamine(Non-covalent)

NZE.2: 17 residues within 4Å: Chain A: V.74, E.75, D.76, D.77, F.83, Y.85, N.139, T.175, G.177, Y.189, Y.312, N.343, L.345, L.366, L.387, L.388 Ligands: NHW.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.83, A:F.83, A:Y.189, A:L.345, A:L.366 Hydrogen bonds: A:Y.85, A:T.175, A:G.177 Water bridges: A:N.139, A:Y.312 pi-Stacking: A:Y.189, A:Y.312

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 7 residues within 4Å: Chain A: L.147, R.148, S.149, K.150, R.151, L.152 Ligands: NHW.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:L.147

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: Y.43, K.158 Ligand excluded by PLIP

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

DMS.5: 7 residues within 4Å: Chain A: E.137, W.267, F.314, V.386, L.387, L.388 Ligands: DMS.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.388 Water bridges: A:E.137 Salt bridges: A:E.137 pi-Cation interactions: A:W.267 DMS.6: 6 residues within 4Å: Chain A: I.122, E.137, W.267, I.385, V.386 Ligands: DMS.5 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:E.137 pi-Cation interactions: A:W.267, A:W.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brannigan, J.A., Plasmodium vivax N-myristoyltransferase with bound indazole inhibitor IMP-923. To Be Published

Release Date

2021-07-21

Peptides

Glycylpeptide N-tetradecanoyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
CCC

Glycylpeptide N-tetradecanoyltransferase

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