SMTL ID : 7tvs.1

The Crystal Structure of SARS-CoV-2 Omicron Mpro (P132H) in complex with demethylated analog of masitinib

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

2 x XNJ: N-(4-methyl-3-{[4-(pyridin-3-yl)-1,3-thiazol-2-yl]amino}phenyl)-4-[(piperazin-1-yl)methyl]benzamide(Non-covalent)

XNJ.1: 15 residues within 4Å: Chain A: T.24, T.25, H.41, C.44, S.46, F.140, L.141, N.142, S.144, C.145, H.163, H.164, M.165, E.166, D.187 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:H.41, A:M.165 Hydrogen bonds: A:T.24, A:H.41, A:H.164, A:E.166 pi-Stacking: A:H.41 XNJ.4: 15 residues within 4Å: Chain B: T.24, T.25, H.41, C.44, S.46, F.140, L.141, N.142, S.144, C.145, H.163, H.164, M.165, E.166, D.187 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:H.41, B:M.165 Hydrogen bonds: B:T.24, B:H.41, B:H.164, B:E.166 pi-Stacking: B:H.41

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

DMS.2: 7 residues within 4Å: Chain A: M.6, A.7, F.8, Q.127, R.298 Chain B: S.123, G.124 2 PLIP interactions: 2 interactions with chain A Water bridges: A:M.6 pi-Cation interactions: A:F.8 DMS.3: 7 residues within 4Å: Chain A: G.15, C.16, M.17, V.18, W.31, A.70, G.71 No protein-ligand interaction detected (PLIP) DMS.5: 7 residues within 4Å: Chain A: S.123, G.124 Chain B: M.6, A.7, F.8, Q.127, R.298 2 PLIP interactions: 2 interactions with chain B Water bridges: B:M.6 pi-Cation interactions: B:F.8 DMS.6: 7 residues within 4Å: Chain B: G.15, C.16, M.17, V.18, W.31, A.70, G.71 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, K. et al., The Crystal Structure of SARS-CoV-2 Omicron Mpro (P132H) in complex with demethylated analog of masitinib. To Be Published

Release Date

2022-02-16

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase nsp5

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