SMTL ID : 8wts.1

SARS-CoV-2 3CLpro bound to covalent inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

monomer

Ligands

1 x XDQ: (2~{R})-2-[[4-[chloranyl-bis(fluoranyl)methoxy]phenyl]-(2-chloranyl-2-fluoranyl-ethanoyl)amino]-~{N}-(oxan-4-yl)-2-pyrimidin-5-yl-propanamide

XDQ.1: 17 residues within 4Å: Chain A: H.41, C.44, M.49, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, D.187, R.188, Q.189 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.143, A:S.144, A:E.166 Water bridges: A:T.190 pi-Stacking: A:H.41

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

EDO.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.3: 3 residues within 4Å: Chain A: Q.69, G.71, N.72 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.69

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

CL.4: 2 residues within 4Å: Chain A: R.4, K.5 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: L.286, L.287 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: Q.74 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain A: L.167, P.168, T.169, A.193, A.194 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Peng, J. et al., SARS-CoV-2 3CLpro bound to covalent inhibitor. To Be Published

Release Date

2025-04-23

Peptides

3C-like proteinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

3C-like proteinase

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