SMTL ID : 6xbg.1

Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor UAW246

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x P6S- LEU- UZ4- UZ1: inhibitor UAW246(Non-covalent)

P6S-LEU-UZ4-UZ1.1: 19 residues within 4Å: Chain A: T.28, H.43, M.51, F.142, L.143, N.144, G.145, S.146, C.147, H.165, H.166, M.167, E.168, P.170, H.174, D.189, Q.191, T.192, A.193 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:H.43, A:P.170, A:D.189, A:A.193 Hydrogen bonds: A:F.142, A:G.145, A:S.146, A:S.146, A:C.147, A:H.166, A:E.168, A:E.168, A:Q.191, A:Q.191 P6S-LEU-UZ4-UZ1.2: 16 residues within 4Å: Chain B: T.28, H.43, M.51, F.142, L.143, N.144, G.145, S.146, C.147, H.165, H.166, M.167, E.168, H.174, D.189, Q.191 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:M.167 Hydrogen bonds: B:F.142, B:G.145, B:S.146, B:C.147, B:H.166, B:E.168, B:E.168, B:Q.191 Water bridges: B:H.43

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain B: S.64, N.65, H.66 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.65, B:N.65 GOL.4: 8 residues within 4Å: Chain B: E.16, G.17, C.18, M.19, V.20, W.33, A.72, K.99 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.16, B:G.17, B:M.19 GOL.5: 4 residues within 4Å: Chain A: K.7 Chain B: F.5, R.6, K.7 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.7, B:K.7, B:K.7 Water bridges: B:R.6

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 1 residues within 4Å: Chain B: L.273 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.273

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sacco, M.D. et al., Structure and inhibition of the SARS-CoV-2 main protease reveal strategy for developing dual inhibitors against M pro and cathepsin L. Sci Adv (2020)

Release Date

2020-06-17

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

Related Entries With Identical Sequence