SMTL ID : 2yne.1 (2 other biounits)

Plasmodium vivax N-myristoyltransferase in complex with a benzothiophene inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

monomer

Ligands

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

DMS.1: 4 residues within 4Å: Chain A: E.133, F.255, W.263, I.381 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:E.133 pi-Cation interactions: A:W.263

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

NHW.2: 34 residues within 4Å: Chain A: Y.2, K.3, F.4, W.5, N.68, Y.69, V.70, V.134, N.135, F.136, L.137, C.138, V.139, R.144, S.145, K.146, R.147, L.148, A.149, P.150, I.153, T.157, I.160, N.161, W.166, Q.167, A.168, Y.170, T.171, A.172, V.174, L.176, Y.367 Ligands: MG.5 37 PLIP interactions: 37 interactions with chain A Hydrophobic interactions: A:W.5, A:W.5, A:Y.69, A:V.134, A:V.134, A:L.137, A:L.137, A:V.139, A:I.153, A:I.160, A:I.160, A:A.168, A:Y.170, A:Y.170, A:Y.367 Hydrogen bonds: A:K.3, A:F.4, A:W.5, A:F.136, A:L.137, A:L.137, A:V.139, A:R.144, A:R.144, A:S.145, A:R.147, A:A.149 Water bridges: A:Y.2, A:Y.2, A:R.144, A:R.144, A:S.145, A:R.147, A:R.147, A:R.147 Salt bridges: A:R.147, A:R.147

1 x YNE: 2-(3-piperidin-4-yloxy-1-benzothiophen-2-yl)-5-[(1,3,5-trimethylpyrazol-4-yl)methyl]-1,3,4-oxadiazole(Non-covalent)

YNE.3: 22 residues within 4Å: Chain A: V.70, E.71, D.72, F.77, R.78, F.79, Y.81, T.171, Y.185, H.187, Y.289, L.291, S.293, Y.308, S.309, N.339, A.340, L.341, L.362, V.382, L.383, L.384 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:V.70, A:Y.185, A:L.291, A:Y.308, A:N.339, A:L.341, A:L.341, A:V.382 Hydrogen bonds: A:Y.81, A:S.293, A:Y.308 Water bridges: A:N.135, A:N.135, A:T.171, A:T.171 pi-Stacking: A:F.79

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

SO4.4: 2 residues within 4Å: Chain A: R.184, K.347 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.184, A:K.347 Salt bridges: A:R.184, A:K.347

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 7 residues within 4Å: Chain A: L.143, R.144, S.145, K.146, R.147, L.148 Ligands: NHW.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:L.143

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

CL.6: 3 residues within 4Å: Chain A: Y.301, S.302, T.303 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: Y.39, K.154 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wright, M.H. et al., Validation of N-Myristoyltransferase as an Antimalarial Drug Target Using an Integrated Chemical Biology Approach. Nat.Chem. (2014)

Release Date

2014-01-15

Peptides

GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE

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