SMTL ID : 7aol.1

Structure of SARS-CoV-2 Main Protease bound to Climbazole

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

homo-dimer

Ligands

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

DMS.1: 3 residues within 4Å: Chain A: Q.74, L.75, R.76 No protein-ligand interaction detected (PLIP) DMS.4: 10 residues within 4Å: Chain A: E.14, G.15, C.16, M.17, V.18, W.31, A.70, G.71, N.95, K.97 No protein-ligand interaction detected (PLIP) DMS.5: 2 residues within 4Å: Chain A: Y.101, F.103 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.103 DMS.6: 10 residues within 4Å: Chain A: M.6, A.7, F.8, S.113, Q.127, D.295, R.298, F.305 Chain B: S.123, G.124 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.298 Salt bridges: A:D.295 pi-Cation interactions: A:F.8 DMS.7: 11 residues within 4Å: Chain A: F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166 Chain B: S.1 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.166 DMS.8: 3 residues within 4Å: Chain B: Q.74, L.75, R.76 No protein-ligand interaction detected (PLIP) DMS.11: 10 residues within 4Å: Chain B: E.14, G.15, C.16, M.17, V.18, W.31, A.70, G.71, N.95, K.97 No protein-ligand interaction detected (PLIP) DMS.12: 2 residues within 4Å: Chain B: Y.101, F.103 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:F.103 DMS.13: 10 residues within 4Å: Chain A: S.123, G.124 Chain B: M.6, A.7, F.8, S.113, Q.127, D.295, R.298, F.305 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.295, B:R.298 Salt bridges: B:D.295 pi-Cation interactions: B:F.8 DMS.14: 11 residues within 4Å: Chain A: S.1 Chain B: F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.166

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 4 residues within 4Å: Chain A: P.96, K.97, T.98, P.99 No protein-ligand interaction detected (PLIP) IMD.9: 4 residues within 4Å: Chain B: P.96, K.97, T.98, P.99 No protein-ligand interaction detected (PLIP)

2 x RQH: (1~{S})-1-(4-chloranylphenoxy)-1-imidazol-1-yl-3,3-dimethyl-butan-2-one(Non-covalent)

RQH.3: 6 residues within 4Å: Chain A: F.103, V.104, R.105, Q.107, D.176, E.178 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.105 RQH.10: 6 residues within 4Å: Chain B: F.103, V.104, R.105, Q.107, D.176, E.178 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:R.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gunther, S. et al., X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease. Science (2021)

Release Date

2020-12-02

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase

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