SMTL ID : 5o4v.1 (2 other biounits)

P.vivax NMT with aminomethylindazole and quinoline inhibitors bound

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: 35 residues within 4Å: Chain A: Y.3, K.4, F.5, W.6, N.69, Y.70, V.71, V.135, N.136, F.137, L.138, C.139, V.140, R.145, S.146, K.147, R.148, L.149, A.150, P.151, I.154, T.158, I.161, N.162, W.167, Q.168, A.169, Y.171, T.172, A.173, V.175, L.177, Y.368 Ligands: 9K2.2, MG.4 37 PLIP interactions: 37 interactions with chain A Hydrophobic interactions: A:W.6, A:W.6, A:Y.70, A:V.135, A:L.138, A:L.138, A:V.140, A:A.150, A:I.154, A:T.158, A:I.161, A:I.161, A:A.169, A:Y.171, A:Y.368 Hydrogen bonds: A:K.4, A:F.5, A:W.6, A:L.138, A:L.138, A:V.140, A:R.145, A:S.146, A:R.148, A:L.149, A:A.150 Water bridges: A:Y.3, A:Y.3, A:R.145, A:R.145, A:R.145, A:R.148, A:R.148, A:R.148, A:R.148 Salt bridges: A:R.148, A:R.148

1 x 9K2: 1-[5-(4-fluoranyl-2-methyl-phenyl)-1~{H}-indazol-3-yl]-~{N},~{N}-dimethyl-methanamine(Non-covalent)

9K2.2: 16 residues within 4Å: Chain A: V.71, F.80, Y.82, N.136, T.172, G.174, Y.186, Y.309, N.340, A.341, L.342, L.363, L.384, L.385 Ligands: NHW.1, 9KZ.8 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.80, A:F.80, A:Y.186, A:Y.186, A:Y.186, A:Y.186, A:N.340, A:L.342 Hydrogen bonds: A:Y.82, A:T.172, A:G.174 Water bridges: A:N.136 pi-Stacking: A:Y.309

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

DMS.3: 5 residues within 4Å: Chain A: I.119, E.134, W.264, I.382, L.384 4 PLIP interactions: 4 interactions with chain A Water bridges: A:L.385 Salt bridges: A:E.134 pi-Cation interactions: A:W.264, A:W.264

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 7 residues within 4Å: Chain A: L.144, R.145, S.146, K.147, R.148, L.149 Ligands: NHW.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:L.144

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

CL.5: 2 residues within 4Å: Chain A: Y.40, K.155 Ligand excluded by PLIP

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

SO4.6: 4 residues within 4Å: Chain A: N.224, T.317, A.318, Q.322 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.317, A:Q.322 SO4.7: 7 residues within 4Å: Chain A: N.270, Y.273, S.291, N.306, N.334, N.335, F.336 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.270, A:Y.273, A:S.291, A:S.291, A:N.334

1 x 9KZ: ethyl 2,4-dimethylquinoline-3-carboxylate(Non-covalent)

9KZ.8: 12 residues within 4Å: Chain A: V.71, E.72, D.73, F.78, F.80, Y.186, H.188, F.201, S.294, L.305, N.340 Ligands: 9K2.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.71, A:D.73, A:F.78, A:F.78, A:F.78, A:Y.186, A:F.201 Hydrogen bonds: A:S.294 Salt bridges: A:H.188 pi-Stacking: A:F.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mousnier, A. et al., Fragment-derived inhibitors of human N-myristoyltransferase block capsid assembly and replication of the common cold virus. Nat Chem (2018)

Release Date

2018-05-16

Peptides

Glycylpeptide N-tetradecanoyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glycylpeptide N-tetradecanoyltransferase

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