SMTL ID : 9r5t.1 (1 other biounit)

NSP14 IN COMPLEX WITH LIGAND TDI-016037-NX-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

3 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

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

SAH.4: 18 residues within 4Å: Chain A: W.293, R.311, G.334, P.336, D.353, A.354, Q.355, L.367, F.368, Y.369, W.386, N.387, C.388, V.390, F.427 Ligands: 01.5, CL.7, EDO.13 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Q.314, A:A.354, A:Q.355, A:Y.369, A:Y.369, A:W.386, A:W.386 Water bridges: A:D.353, A:Q.355, A:W.386, A:N.389, A:N.389 Salt bridges: A:R.311

1 x 01: ~{N}-[(1-cyclopropyl-6-fluoranyl-indazol-7-yl)methyl]-1,5-dimethyl-4-[(7-methyl-2~{H}-indazol-5-yl)sulfonyl]pyrrole-2-carboxamide

01.5: 20 residues within 4Å: Chain A: W.293, N.307, R.311, N.335, P.336, K.337, I.339, N.387, N.389, F.402, Y.421, N.423, K.424, H.425, F.427, H.428, T.429, F.507 Ligands: SAH.4, EDO.13 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.339, A:N.387, A:F.402, A:Y.421, A:N.423, A:F.427, A:F.427, A:F.427, A:F.507 Hydrogen bonds: A:R.311, A:H.428 Water bridges: A:K.424 pi-Stacking: A:F.427 pi-Cation interactions: A:R.311

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

CL.6: 1 residues within 4Å: Chain A: N.411 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: K.289, A.354 Ligands: SAH.4, EDO.13 Ligand excluded by PLIP

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 4 residues within 4Å: Chain A: Y.362, I.364, E.365 Ligands: EDO.9 3 PLIP interactions: 3 interactions with chain A Water bridges: A:I.364, A:E.365, A:E.366 EDO.9: 1 residues within 4Å: Ligands: EDO.8 No protein-ligand interaction detected (PLIP) EDO.10: 6 residues within 4Å: Chain A: K.176, N.177, L.178, S.179, D.180, I.300 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.177 EDO.11: 4 residues within 4Å: Chain A: T.251, S.256, N.257, L.260 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.256 EDO.12: 7 residues within 4Å: Chain A: R.77, H.284, E.285, C.286, F.287, K.289, R.290 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.284, A:K.289, A:R.290, A:R.290 Water bridges: A:D.292 EDO.13: 8 residues within 4Å: Chain A: F.287, V.288, R.290, V.291, H.428 Ligands: SAH.4, 01.5, CL.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.288 Water bridges: A:H.428 EDO.14: 3 residues within 4Å: Chain A: K.201, F.218, Y.225 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.225

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.15: 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:Y.495, A:Y.495 pi-Stacking: A:F.446

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meyer, C. et al., Discovery of Novel Isofunctional SARS-CoV-2 NSP14 RNA Cap Methyltransferase Inhibitors by Structure-Based Virtual Screening. Acs Med.Chem.Lett. (2025)

Release Date

2025-08-27

Peptides

Guanine-N7 methyltransferase nsp14: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Guanine-N7 methyltransferase nsp14

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