SMTL ID : 6m0k.1

The crystal structure of COVID-19 main protease in complex with an inhibitor 11b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

8 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 7 residues within 4Å: Chain A: G.15, M.17, V.18, W.31, A.70, G.71, K.97 No protein-ligand interaction detected (PLIP) DMS.2: 8 residues within 4Å: Chain A: M.165, E.166, P.168, R.188, Q.189, T.190, Q.192 Ligands: FJC.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.190, A:Q.192 DMS.3: 3 residues within 4Å: Chain A: Y.118, L.141 Chain B: R.298 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.123 DMS.4: 6 residues within 4Å: Chain A: M.6, A.7, F.8, Q.127, R.298 Chain B: S.123 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.298 Water bridges: A:M.6 pi-Cation interactions: A:F.8 DMS.6: 7 residues within 4Å: Chain B: G.15, M.17, V.18, W.31, A.70, G.71, K.97 No protein-ligand interaction detected (PLIP) DMS.7: 8 residues within 4Å: Chain B: M.165, E.166, P.168, R.188, Q.189, T.190, Q.192 Ligands: FJC.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.190, B:Q.192 DMS.8: 3 residues within 4Å: Chain A: R.298 Chain B: Y.118, L.141 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.123 DMS.9: 6 residues within 4Å: Chain A: S.123 Chain B: M.6, A.7, F.8, Q.127, R.298 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.298 Water bridges: B:M.6 pi-Cation interactions: B:F.8

2 x FJC: ~{N}-[(2~{S})-3-(3-fluorophenyl)-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide(Covalent)

FJC.5: 18 residues within 4Å: Chain A: H.41, M.49, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, H.172, V.186, D.187, R.188, Q.189 Ligands: DMS.2 9 PLIP interactions: 1 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:S.1, A:G.143, A:S.144, A:C.145, A:H.164, A:E.166, A:E.166 Hydrophobic interactions: A:M.165 Halogen bonds: A:Q.189 FJC.10: 18 residues within 4Å: Chain B: H.41, M.49, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, H.172, V.186, D.187, R.188, Q.189 Ligands: DMS.7 11 PLIP interactions: 2 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:S.1, A:S.1, B:G.143, B:S.144, B:C.145, B:H.164, B:E.166, B:E.166, B:E.166 Hydrophobic interactions: B:M.165 Halogen bonds: B:Q.189

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dai, W. et al., Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease. Science (2020)

Release Date

2020-04-29

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase

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