MolNFT v1 · #175789 · protein

Crystal structure of SARS-cov-2 main protease with narlaprevir

7D1O · 3C-like proteinase: “Crystal structure of SARS-cov-2 main protease with narlaprevir”. X-ray diffraction, 1 ligand (NNA), 2 pockets (best druggability 0.52). MolNFT v1 #175789 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 7D1O
Type: protein
Length: 301 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3C-like proteinase
EC: 3.4.22.69
UniProt: P0DTC1
Ligands: NNA
Pockets: 2 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3C-like proteinase (EC 3.4.22.69)	protein	301	26% helix, 29% strand	P0DTC1

Ligands and binding sites

NNA · (1R,2S,5S)-3-[N-({1-[(tert-butylsulfonyl) methyl]cyclohexyl}carbamoyl)-3-methyl-L-valyl]-N-{(1S)-1-[(1R)-2-(cyclopropylamino)-1-hydroxy-2-oxoethyl]pentyl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	219	0.52	0.76	27	NNA
2	54	0.37	0.80	13	empty

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

7D1O · Crystal structure of SARS-Cov-2 main protease with narlaprevir · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P0DTC1
Elsewhere: RCSB PDB 7D1O · PDBe 7D1O · UniProt P0DTC1

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