SMTL ID : 9r5t.2 (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

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.11: 4 residues within 4Å: Chain A: C.209 Ligands: IMD.5, IMD.6, IMD.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.209

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: 01.8, CL.9, IPA.20 12 PLIP interactions: 12 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 Salt bridges: A:R.311

4 x IMD: IMIDAZOLE(Non-covalent)

IMD.5: 4 residues within 4Å: Chain A: C.209 Ligands: IMD.6, IMD.7, ZN.11 No protein-ligand interaction detected (PLIP) IMD.6: 6 residues within 4Å: Chain A: R.206, C.209, D.223 Ligands: IMD.5, IMD.7, ZN.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.223 Water bridges: A:R.206 IMD.7: 6 residues within 4Å: Chain A: T.207, C.208, C.209 Ligands: IMD.5, IMD.6, ZN.11 No protein-ligand interaction detected (PLIP) IMD.18: 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:P.444, A:F.446, A:Y.495 pi-Stacking: A:F.446

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

01.8: 19 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 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:K.337, 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:N.389 pi-Stacking: A:F.427 pi-Cation interactions: A:R.311

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

CL.9: 3 residues within 4Å: Chain A: K.289, A.354 Ligands: SAH.4 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain A: T.404, R.405, V.406, L.407, N.411 Ligand excluded by PLIP

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

EDO.12: 4 residues within 4Å: Chain A: K.201, F.218, T.220, Y.236 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.201, A:K.201 EDO.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.14: 5 residues within 4Å: Chain A: D.325, K.326, F.327, P.328, G.381 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.325, A:G.381 EDO.15: 4 residues within 4Å: Chain A: W.293, T.294, C.357 Ligands: IPA.22 No protein-ligand interaction detected (PLIP) EDO.16: 3 residues within 4Å: Chain A: Y.352, K.377, F.378 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.378 Water bridges: A:T.379 EDO.17: 5 residues within 4Å: Chain A: W.87, S.113, T.114, R.279, P.413 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.113 Water bridges: A:W.87

4 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.19: 6 residues within 4Å: Chain A: S.172, D.173, K.176, W.228, H.229, S.231 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.176, A:W.228 IPA.20: 5 residues within 4Å: Chain A: V.288, V.291, F.427, H.428 Ligands: SAH.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.291 Hydrogen bonds: A:H.428 Water bridges: A:A.426 IPA.21: 2 residues within 4Å: Chain A: L.304, K.424 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.424 IPA.22: 6 residues within 4Å: Chain A: R.290, V.291, D.292, W.293, T.294 Ligands: EDO.15 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.294 Hydrogen bonds: A:W.293

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

SO4.23: 2 residues within 4Å: Chain A: A.472, N.479 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.472, A:N.479 SO4.24: 2 residues within 4Å: Chain A: Y.518, W.521 No protein-ligand interaction detected (PLIP)

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
B

Guanine-N7 methyltransferase nsp14

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