SMTL ID : 8r7b.2 (1 other biounit)

SARS-CoV-2 NSP14 in complex with SAH and TDI-015051

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

monomer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.208, C.211, C.227, H.230 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.208, A:C.211, A:C.227, A:H.230 ZN.2: 4 residues within 4Å: Chain A: H.258, C.262, H.265, C.280 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.258, A:C.262, A:H.265, A:C.280 ZN.3: 4 residues within 4Å: Chain A: C.453, C.478, C.485, H.488 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.453, A:C.478, A:C.485, A:H.488 ZN.12: 4 residues within 4Å: Chain A: C.209 Ligands: IMD.4, IMD.5, IMD.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.209

4 x IMD: IMIDAZOLE(Non-covalent)(Non-functional Binders)

IMD.4: 4 residues within 4Å: Chain A: C.209 Ligands: IMD.5, IMD.6, ZN.12 No protein-ligand interaction detected (PLIP) IMD.5: 7 residues within 4Å: Chain A: R.206, C.209, D.223, Y.225 Ligands: IMD.4, IMD.6, ZN.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.206, A:D.223 IMD.6: 3 residues within 4Å: Ligands: IMD.4, IMD.5, ZN.12 No protein-ligand interaction detected (PLIP) IMD.13: 9 residues within 4Å: Chain A: V.313, V.317, L.443, P.444, F.445, F.446, Y.495, Y.499, L.509 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.446, A:F.446, A:Y.495 pi-Stacking: A:F.446

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.7: 15 residues within 4Å: Chain A: W.293, R.311, G.334, P.336, D.353, A.354, L.367, F.368, Y.369, W.386, N.387, C.388, V.390, F.427 Ligands: YDT.14 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.314, A:A.354, A:Q.355, A:Y.369, A:Y.369, A:W.386 Water bridges: A:D.353, A:W.386 Salt bridges: A:R.311

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

CL.8: 3 residues within 4Å: Chain A: E.296, Y.297, P.298 Ligand excluded by PLIP CL.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: T.404, N.411 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: K.289, A.354 Ligand excluded by PLIP

1 x YDT: N-[(5-fluoranyl-1-benzofuran-4-yl)methyl]-1,5-dimethyl-4-(1,4,6,7-tetrahydropyrazolo[4,3-c]pyridin-5-ylsulfonyl)pyrrole-2-carboxamide(Non-covalent)

YDT.14: 17 residues within 4Å: Chain A: W.293, N.307, R.311, N.335, P.336, K.337, I.339, N.387, N.389, Y.421, N.423, K.424, H.425, F.427, T.429, F.507 Ligands: SAH.7 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:K.337, A:K.337, A:N.387, A:Y.421, A:Y.421, A:N.423, A:F.427, A:F.427, A:F.427 Hydrogen bonds: A:R.311, A:N.387, A:N.389, A:T.429 pi-Cation interactions: A:R.311

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meyer, C. et al., Small-molecule inhibition of SARS-CoV-2 guanine-N7 RNA cap methyltransferase. To Be Published

Release Date

2024-10-23

Peptides

Guanine-N7 methyltransferase nsp14: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Guanine-N7 methyltransferase nsp14

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