SMTL ID : 5o6h.1 (1 other biounit)

Human NMT1 in complex with myristoyl-CoA and inhibitor IMP-917

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.29 Å

Oligo State

monomer

Ligands

1 x MYA: TETRADECANOYL-COA(Non-covalent)

MYA.1: 35 residues within 4Å: Chain A: Y.12, Q.13, F.14, W.15, N.74, Y.75, V.76, I.140, N.141, F.142, L.143, C.144, V.145, R.150, S.151, K.152, R.153, V.154, A.155, P.156, I.159, T.163, V.166, H.167, I.171, F.172, Q.173, A.174, Y.176, T.177, A.178, L.182, Y.374 Ligands: 9M2.5, MG.6 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:W.15, A:W.15, A:Y.75, A:V.76, A:I.140, A:L.143, A:L.143, A:V.145, A:A.155, A:I.159, A:I.159, A:V.166, A:A.174, A:Y.176, A:Y.176, A:Y.374 Hydrogen bonds: A:Q.13, A:F.14, A:W.15, A:F.142, A:L.143, A:L.143, A:V.145, A:R.150, A:R.150, A:S.151, A:R.153, A:V.154, A:A.155 Water bridges: A:S.151, A:R.153 Salt bridges: A:R.153, A:R.153

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 2 residues within 4Å: Chain A: E.34, K.37 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.34 Water bridges: A:Q.18, A:K.37 Salt bridges: A:K.37 PO4.3: 5 residues within 4Å: Chain A: Y.45, T.46, V.157, R.160 Ligands: DMS.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.46, A:T.46 Water bridges: A:R.160, A:R.160 Salt bridges: A:R.160 PO4.4: 5 residues within 4Å: Chain A: Q.13, F.14, R.153, P.156, R.160 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.13 Water bridges: A:R.160, A:R.160 Salt bridges: A:R.153, A:R.160

1 x 9M2: 1-[5-[4-fluoranyl-2-[2-(1,3,5-trimethylpyrazol-4-yl)ethoxy]phenyl]-2~{H}-indazol-3-yl]-~{N},~{N}-dimethyl-methanamine(Non-covalent)

9M2.5: 19 residues within 4Å: Chain A: V.76, E.77, D.78, F.83, F.85, Y.87, N.141, T.177, Y.191, F.206, S.300, Y.315, N.346, A.347, L.348, L.369, L.390, Q.391 Ligands: MYA.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.76, A:F.85, A:Y.191, A:Y.191, A:F.206, A:L.348 Hydrogen bonds: A:T.177, A:S.300 Water bridges: A:N.141, A:G.179, A:G.179, A:Y.315 pi-Stacking: A:Y.315

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 7 residues within 4Å: Chain A: L.149, R.150, S.151, K.152, R.153, V.154 Ligands: MYA.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:L.149

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 11 residues within 4Å: Chain A: P.21, K.184, P.185, V.186, Y.372, L.373, W.376, K.377, C.378, P.379, S.380 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:P.185, A:L.373, A:L.373, A:C.378, A:C.378 Water bridges: A:K.184, A:S.380

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

DMS.8: 1 residues within 4Å: Ligands: PO4.3 No protein-ligand interaction detected (PLIP)

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 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glycylpeptide N-tetradecanoyltransferase 1

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