6XHL: 3C-like proteinase

Covalent complex of SARS-CoV main protease with N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide. Determined by X-ray diffraction at 1.47 Å resolution. Released 8 Jul 2020.

Method: X-ray diffraction
Resolution: 1.47 Å
Organism: Human SARS coronavirus
Chains: 2
Atoms: 5,122
Mol. weight: 68.82 kDa
Ligands: V2M
Released: 8 Jul 2020

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

Secondary structure: helices and β-sheets

6XHL contains 34 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	66-70	5	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	121-129	9	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	293-301	9

Chain B: 18 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	47-50	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
α-helix	98-99	2
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	240-242	3
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

>6XHL_1 3C-like proteinase (chains A, B)
GSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLI
RKSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYN
GSPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG
KFYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNY
EPLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQ
CSGVTFQ

Ligands and cofactors

ID	Name	Formula	Copies
V2M	N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino…	C24 H34 N4 O6	2

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:

6XHN 1.38 Å, Covalent complex of SARS-CoV main protease with 4-methoxy-N-[(2S)-4-methyl-1-oxo-1-({(2S)…
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…
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

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