9NME: SARS-CoV-2 3CLPro

SARS-CoV-2 3CLPro in complex with 2-[2-hydroxy-3-(4-isoquinolyl)-4-oxo-6-(trifluoromethyl)-1H-quinolin-8-yl]benzonitrile. Determined by X-ray diffraction at 1.6 Å resolution. Released 18 Mar 2026.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Severe acute respiratory syndrome coronavirus 2
Chains: 1
Atoms: 2,672
Mol. weight: 62.54 kDa
Ligands: A1BY3
Released: 18 Mar 2026

Explore 9NME in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9NME contains 16 α-helices and 19 β-strands across 1 chain. 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, 19 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	11-14	4
β-strand	17-22	6	1
β-strand	25-32	8	1
β-strand	35-39	5	1
α-helix	40-43	4
α-helix	54-59	6
α-helix	63-65	3
β-strand	66-70	5	1
β-strand	73-75	3	1
β-strand	77-83	7	1
β-strand	86-91	6	1
α-helix	98-99	2
β-strand	100-103	4	2
α-helix	106-107	2
β-strand	111-118	8	2
β-strand	121-129	9	2
β-strand	136	1	2
β-strand	148-153	6	2
β-strand	156-166	11	2
β-strand	172-175	4	2
α-helix	180	1
β-strand	181	1	2
α-helix	193-197	5
β-strand	199	1	3
α-helix	201-213	13
α-helix	227-236	10
β-strand	239	1	3
α-helix	240-242	3
α-helix	244-249	6
α-helix	251-257	7
α-helix	261-274	14
β-strand	281	1	4
β-strand	284	1	4
α-helix	293-299	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutathione S-transferase class-mu 26 kDa isozyme,Replicase polyprotein 1ab	A	protein	549	Severe acute respiratory syndrome coronavirus 2	P08515 (AlphaFold model), P0DTD1 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9NME_1 Glutathione S-transferase class-mu 26 kDa isozyme,Replicase polyprotein 1ab (chains A)
MSPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKFELGLEFPNLPYYID
GDVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAVLDIRYGVSRIAYSKDFETLKV
DFLSKLPEMLKMFEDRLCHKTYLNGDHVTHPDFMLYDALDVVLYMDPMCLDAFPKLVCFK
KRIEAIPQIDKYLKSSKYIAWPLQGWQATFGGGDHPPKSDLEVLFQGPLGSAVLQSGFRK
MAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHN
FLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGV
YQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPF
VDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQD
HVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTF
QGPHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
A1BY3	(2M)-2-[(3P)-2-hydroxy-3-(isoquinolin-4-yl)-4-oxo-6-(trifluoromethyl)-1,4-dihyd…	C26 H14 F3 N3 O2	1

Primary citation

Structure Based Design of non-covalent, non-peptidic inhibitors of SARS-CoV-2 Main Protease. Goins, C.M., Stauffer, S.R., Rodzinak, K. To be published.

Other PDB entries of the same protein (UniProt P08515 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8OK1 1.38 Å, WD repeat containing protein 5 (WDR5)- N225A mutant
6JI6 1.5 Å, Crystal structure of glutathione S-transferase complexed and modified with glutathione
6RWD 1.53 Å, Crystal structure of SjGST in complex with GSH and ellagic acid at 1.53 Angstrom…
4WR4 1.6 Å, Crystal Structure of GST Mutated with Halogenated Tyrosine (7bGST-1)
8GYD 1.7 Å, Structure of Schistosoma japonicum Glutathione S-transferase bound with the ligand…
9N4U 1.77 Å, Crystal structure of PAK1 bound to compound R1
1DUG 1.8 Å, Structure of the fibrinogen G chain integrin binding and factor xiiia crosslinking sites…
9NMF 1.8 Å, SARS-CoV-2 3CLPro in complex with 8-(6-amino-3-pyridyl)-2-hydroxy-3-(4-isoquinolyl)-6-(tr…
7AL7 1.8 Å, The Crystal Structure of Human IL-18 in Complex With Human IL-18 Binding Protein
8OKF 1.85 Å, WD repeat containing protein 5 (WDR5)- PER2 peptide
9N48 1.85 Å, Crystal structure of PAK1 bound to compound C1
3CRT 1.9 Å, Structural characterization of an engineered allosteric protein

Browse structure collections

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