6XHN: 3C-like proteinase

Covalent complex of SARS-CoV main protease with 4-methoxy-N-[(2S)-4-methyl-1-oxo-1-({(2S)-3-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)pentan-2-yl]-1H-indole-2-carboxamide. Determined by X-ray diffraction at 1.38 Å resolution. Released 8 Jul 2020.

Method: X-ray diffraction
Resolution: 1.38 Å
Organism: Human SARS coronavirus
Chains: 2
Atoms: 5,175
Mol. weight: 69.13 kDa
Ligands: V3D
Released: 8 Jul 2020

Explore 6XHN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6XHN contains 32 α-helices and 40 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 16 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	1
α-helix	8-9	2
α-helix	11-14	4
β-strand	17-22	6	2
β-strand	25-32	8	2
β-strand	35-39	5	2
α-helix	40-43	4
α-helix	48-50	3
α-helix	54-59	6
α-helix	63-65	3
β-strand	67-70	4	2
β-strand	73-75	3	2
β-strand	77-83	7	2
β-strand	86-91	6	2
β-strand	100-103	4	3
α-helix	106-107	2
β-strand	111-118	8	3
β-strand	121-130	10	3
β-strand	136	1	3
β-strand	148-153	6	3
β-strand	156-166	11	3
β-strand	172-175	4	3
α-helix	180	1
β-strand	181	1	3
α-helix	194-197	4
β-strand	199	1	4
α-helix	201-213	13
α-helix	227-236	10
β-strand	239	1	4
α-helix	240-243	4
α-helix	244-249	6
α-helix	251-257	7
α-helix	261-274	14
β-strand	281	1	5
β-strand	284	1	5
α-helix	293-300	8

Chain B: 16 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	3
α-helix	8-9	2
α-helix	11-14	4
β-strand	17-22	6	6
β-strand	25-32	8	6
β-strand	35-39	5	6
α-helix	40-43	4
α-helix	54-59	6
α-helix	63-65	3
β-strand	67-70	4	6
β-strand	73-75	3	6
β-strand	77-83	7	6
β-strand	86-91	6	6
β-strand	100-103	4	1
α-helix	106-107	2
β-strand	111-118	8	1
β-strand	121-129	9	1
β-strand	136	1	1
β-strand	148-153	6	1
β-strand	156-166	11	1
β-strand	172-175	4	1
α-helix	180	1
β-strand	181	1	1
α-helix	194-197	4
β-strand	199	1	7
α-helix	201-213	13
α-helix	227-236	10
β-strand	239	1	7
α-helix	240-243	4
α-helix	244-249	6
α-helix	251-257	7
α-helix	261-274	14
β-strand	281	1	8
β-strand	284	1	8
α-helix	287-288	2
α-helix	293-300	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
3C-like proteinase	A, B	protein	307	Human SARS coronavirus	P0C6U8

Sequence of entity 1 (A, B), FASTA

>6XHN_1 3C-like proteinase (chains A, B)
GSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLI
RKSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYN
GSPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG
KFYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNY
EPLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQ
CSGVTFQ

Ligands and cofactors

ID	Name	Formula	Copies
V3D	(3S)-3-{[N-(4-methoxy-1H-indole-2-carbonyl)-L-leucyl]amino}-2-oxo-4-[(3S)-2-oxo…	C32 H35 N5 O7	2

Water and common crystallization additives (EDO) are not listed.

Primary citation

Discovery of Ketone-Based Covalent Inhibitors of Coronavirus 3CL Proteases for the Potential Therapeutic Treatment of COVID-19. Hoffman, R.L., Kania, R.S., Brothers, M.A. et al. J Med Chem (2020) 63:12725-12747. DOI 10.1021/acs.jmedchem.0c01063 · PubMed

Other PDB entries of the same protein (UniProt P0C6U8), best resolution first:

4M0W 1.4 Å, Crystal Structure of SARS-CoV papain-like protease C112S mutant in complex with ubiquitin
6XHO 1.45 Å, Covalent complex of SARS-CoV main protease with ethyl (4R)-4-({N-[(4-methoxy-1H-indol-2-y…
6XHL 1.47 Å, Covalent complex of SARS-CoV main protease with N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)…
4MDS 1.6 Å, Discovery of N-(benzo[1,2,3]triazol-1-yl)-N-(benzyl)acetamido)phenyl) carboxamides as…
2H2Z 1.6 Å, Crystal structure of SARS-CoV main protease with authentic N and C-termini
7LMG 1.6 Å, SARS-CoV-1 3CLPro in complex with N-(4-(1H-imidazol-4-yl)phenyl)-2-(1H-benzo[d][1,2,3]tri…
7RC1 1.63 Å, X-ray Structure of SARS-CoV main protease covalently modified by compound GRL-0686
5Y3E 1.65 Å, Crystal structure of SARS coronavirus papain-like protease in complex with glycerol
5Y3Q 1.65 Å, Crystal structure of SARS coronavirus papain-like protease conjugated with…
6W2A 1.65 Å, 1.65 A resolution structure of SARS-CoV 3CL protease in complex with inhibitor 7j
7LMJ 1.69 Å, SARS-CoV-1 3CLPro in complex with 2-(1H-benzo[d][1,2,3]triazol-1-yl)-N-(3-chlorobenzyl)-N…
2DUC 1.7 Å, Crystal structure of SARS coronavirus main proteinase(3CLPRO)

Browse structure collections

About this viewer

MolViewer shows 6XHN directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.