Structure for small-molecule inhibitors of cysteine peptidases (unassigned)

Summary Structure

PDB	Organism	Resolution	Comment
2Q6F	avian infectious bronchitis virus	2.00 Å	complex with Michael acceptor inhibitor N3
One monomer of the dimer is shown. The catalytic residues are shown in ball-and-stick representation: His2797 in purple and Cys2939 in yellow. The bound Michael acceptor N3 inhibitor is shown in grey ball-and-stick representation.

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TERTIARY STRUCTURE DATA
Comment	Resolution	PDB	PDBe	SCOP	CATH	PDBSum	Proteopedia	Reference
avian infectious bronchitis coronavirus 3C-like peptidase ( avian infectious bronchitis virus)
complex with Michael acceptor inhibitor N3	2.00 Å	2Q6F	2Q6F	2Q6F	2Q6F	2Q6F	2Q6F	Xue et al., 2008
sortase B ( Bacillus anthracis)
complex with AAEK1	2.10 Å	2OQW	2OQW	2OQW	2OQW	2OQW	2OQW	Maresso et al., 2007
complex with AAEK2	1.60 Å	2OQZ	2OQZ	2OQZ	2OQZ	2OQZ	2OQZ	Maresso et al., 2007
porcine transmissible gastroenteritis virus-type main peptidase ( feline infectious peritonitis virus)
complex with N-(tert-butoxycarbonyl)-L-seryl-L-valyl-N-(2S)-5-ethoxy-5-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]pentan-2-yl-L-leucinamide inhibitor	2.06 Å	4ZRO	4ZRO	4ZRO	4ZRO	4ZRO	4ZRO	St et al., 2015
cathepsin K ( Homo sapiens)
complex with 1-[N[(phenylmethoxy)carbonyl]-l-leucyl-4-[[N/N-[(phenylmethoxy)carbonyl]-/NL-leucyl]amino]-3-pyrrolidinone	2.50 Å	1AU3	1AU3	1AU3	1AU3	1AU3	1AU3	Marquis et al., 1998
complex with 4-[[N-[(phenylmethoxy)carbonyl]-L-leucyl]amino]-1[(2S)-2-[[[4-(pyridinylmethoxy)carbonyl]amino]-4-methylpentyl]-3-pyrrolidinone	2.30 Å	1AU4	1AU4	1AU4	1AU4	1AU4	1AU4	Marquis et al., 1998
complex with 1,5-bis(N-benzyloxycarbonyl-L-leucinyl)carbohydrazide	2.20 Å	1AYU	1AYU	1AYU	1AYU	1AYU	1AYU	Thompson et al., 1997
complex with N-[2-[1-(N-benzyloxycarbonylamino)-3-methylbutyl]thiazol-4-ylcarbonyl]-N'-(benzyloxycarbonyl-L-leucinyl)hydrazide	2.30 Å	1AYV	1AYV	1AYV	1AYV	1AYV	1AYV	Thompson et al., 1997
complex with 1-(N-benzyloxycarbonyl-L-leucinyl)-5-(3-benzyloxy benzoyl)carbohydrazide	2.40 Å	1AYW	1AYW	1AYW	1AYW	1AYW	1AYW	Thompson et al., 1997
caspase-3 ( Homo sapiens)
complex with nicotinic acid aldehyde (3S)-3-[(5-bromopyridin-3-yl)carbonyl]amino-4-oxobutanoic acid	2.50 Å	1RE1	1RE1	1RE1	1RE1	1RE1	1RE1	Becker et al., 2004
complex with pryazinone inhibitor 3-(2-5-tert-butyl-3-[(4-methyl-furazan-3-ylmethyl)-amino]-2-oxo-2H-pyrazin-1-yl-butyrylamino)-5-(hexyl-methyl-amino)-4-oxo-pentanoic acid anion	2.20 Å	1RHJ	1RHJ	1RHJ	1RHJ	1RHJ	1RHJ	Becker et al., 2004
complex with phenyl- propyl-ketone N-acetyl-L-alpha-aspartyl-L-alpha-glutamyl-N-[(1S)-1-(carboxymethyl)-2-oxo-5-phenylpentyl]-L-valinamide	2.50 Å	1RHK	1RHK	1RHK	1RHK	1RHK	1RHK	Becker et al., 2004
complex with nicotinic acid aldehyde 4-[5-(2-carboxy-1-formyl-ethylcarbamoyl)-pyridin-3-yl]-benzoic acid	2.50 Å	1RHM	1RHM	1RHM	1RHM	1RHM	1RHM	Becker et al., 2004
complex with bromomethoxyphenyl inhibitor 5-S-benzyl-3-(N-[(5-bromo-2-methoxyphenyl)acetyl]- L-valylamino)-2,3-dideoxy-5-thio-D-erythro- pentonic acid	3.00 Å	1RHQ	1RHQ	1RHQ	1RHQ	1RHQ	1RHQ	Becker et al., 2004
complex with cinnamic acid methyl ester (3S)-5-[(2-chloro-6-fluorobenzyl)sulfanyl]-3-[N-(2-ethoxy-5-[(1E)-3-methoxy-3-oxoprop-1-enyl]phenylacetyl)-D-valyl]amino-4-oxopentanoic acid	3.00 Å	1RHR	1RHR	1RHR	1RHR	1RHR	1RHR	Becker et al., 2004
complex with 5,6,7 tricyclic peptidomimetic inhibitor (3S)-3-[((2S)-5-[(N-acetyl-L-alpha-aspartyl)amino]-4-oxo-1,2,4,5,6,7-hexahydroazepino[3,2,1-hi]indol-2-ylcarbonyl)amino]-5-(benzylsulfanyl)-4-oxopentanoic acid	2.51 Å	1RHU	1RHU	1RHU	1RHU	1RHU	1RHU	Becker et al., 2004
cathepsin K ( Homo sapiens)
complex with cyanopyrrolidine inhibitor N2-[(benzyloxy)carbonyl]-N1-[(3S)-1-cyanopyrrolidin-3-yl]-L-leucinamide	2.50 Å	1YK7	1YK7	1YK7	1YK7	1YK7	1YK7	Deaton et al., 2005
complex with cyanamide-based inhibitor tert-butyl 2-cyano-2-methylhydrazinecarboxylate	2.60 Å	1YK8	1YK8	1YK8	1YK8	1YK8	1YK8	Barrett et al., 2005
complex with myocrisin	2.00 Å	2ATO	2ATO	2ATO	2ATO	2ATO	2ATO	Weidauer et al., 2007
cathepsin S ( Homo sapiens)
complex with non-covalent 2-(benzoxazol-2- ylamino)-acetamide	1.90 Å	2F1G	2F1G	2F1G	2F1G	2F1G	2F1G	Tully et al., 2006
caspase-1 ( Homo sapiens)
complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)- propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK)	1.80 Å	2HBQ	2HBQ	2HBQ	2HBQ	2HBQ	2HBQ	Scheer et al., 2006
cathepsin S ( Homo sapiens)
complex with N-[(1R)-1-[(benzylsulfonyl)methyl]-2-[(1S)-1-methyl-2-[4-(trifluoromethoxy)phenyl]aminoethyl]amino-2-oxoethyl]morpholine-4-carboxamide	1.80 Å	2HH5	2HH5	2HH5	2HH5	2HH5	2HH5	Tully et al., 2006
complex with non covalent arylaminoethyl amide.	1.55 Å	2HHN	2HHN	2HHN	2HHN	2HHN	2HHN	Tully et al., 2006
complex with a novel 2- arylphenoxyacetaldehyde inhibitor derived by the substrate activity screening (sas) method	1.60 Å	2OP3	2OP3	2OP3	2OP3	2OP3	2OP3	Inagaki et al., 2007
HIV-1 retropepsin ( human immunodeficiency virus 1)
wild type; complex with GRL-001	1.48 Å	6MCR	6MCR	6MCR	6MCR	6MCR	6MCR
subfamily T1A unassigned peptidases ( Saccharomyces cerevisiae)
20S open-gate proteasome; complex with PR-957 (morpholine)	3.40 Å	3UN4	3UN4	3UN4	3UN4	3UN4	3UN4	Huber et al., 2012
proteasome subunit alpha 4 ( Saccharomyces cerevisiae)
20S open-gate proteasome; complex with PR-957 (morpholine)	3.40 Å	3UN4	3UN4	3UN4	3UN4	3UN4	3UN4	Huber et al., 2012
subfamily T1A non-peptidase homologues ( Saccharomyces cerevisiae)
20S open-gate proteasome; complex with PR-957 (morpholine)	3.40 Å	3UN4	3UN4	3UN4	3UN4	3UN4	3UN4	Huber et al., 2012
subfamily T1A unassigned peptidases ( Saccharomyces cerevisiae)
20S open-gate proteasome; complex with PR-957 (morpholine)	3.40 Å	3UN4	3UN4	3UN4	3UN4	3UN4	3UN4	Huber et al., 2012
proteasome subunit alpha 1 ( Saccharomyces cerevisiae)
20S open-gate proteasome; complex with PR-957 (morpholine)	3.40 Å	3UN4	3UN4	3UN4	3UN4	3UN4	3UN4	Huber et al., 2012
family T1 unassigned peptidases ( Saccharomyces cerevisiae)
20S open-gate proteasome; complex with PR-957 (morpholine)	3.40 Å	3UN4	3UN4	3UN4	3UN4	3UN4	3UN4	Huber et al., 2012
proteasome subunit alpha 6 ( Saccharomyces cerevisiae)
20S open-gate proteasome; complex with PR-957 (morpholine)	3.40 Å	3UN4	3UN4	3UN4	3UN4	3UN4	3UN4	Huber et al., 2012
subfamily T1A non-peptidase homologues ( Saccharomyces cerevisiae)
20S open-gate proteasome; complex with PR-957 (morpholine)	3.40 Å	3UN4	3UN4	3UN4	3UN4	3UN4	3UN4	Huber et al., 2012
proteasome subunit beta 2 ( Saccharomyces cerevisiae)
20S open-gate proteasome; complex with PR-957 (morpholine)	3.40 Å	3UN4	3UN4	3UN4	3UN4	3UN4	3UN4	Huber et al., 2012
20S proteasome component beta 6 ( Saccharomyces cerevisiae)
20S open-gate proteasome; complex with PR-957 (morpholine)	3.40 Å	3UN4	3UN4	3UN4	3UN4	3UN4	3UN4	Huber et al., 2012
psmB4-2 g.p. (Dictyostelium discoideum) ( Saccharomyces cerevisiae)
20S open-gate proteasome; complex with PR-957 (morpholine)	3.40 Å	3UN4	3UN4	3UN4	3UN4	3UN4	3UN4	Huber et al., 2012
SARS coronavirus picornain 3C-like peptidase ( SARS coronavirus)
complex with inhibitor N1	2.00 Å	1WOF	1WOF	1WOF	1WOF	1WOF	1WOF	Yang et al., 2005
complex with N-((3S,6R)-6-((S,E)-4-ethoxycarbonyl-1-((S)-2-oxopyrrolidin-3-yl)but-3-en-2-ylcarbamoyl)-2,9-dimethyl-4-oxodec-8-en-3-yl)-5-methylisoxazole-3-carboxamide	1.90 Å	2ALV	2ALV	2ALV	2ALV	2ALV	2ALV	Ghosh et al., 2005
complex with an inhibitor N9	1.85 Å	2AMD	2AMD	2AMD	2AMD	2AMD	2AMD	Yang et al., 2005
complex with ethyl (2E,4S)-4-[((2R)-2-[N-(tert-butoxycarbonyl)-L-valyl]amino-2-phenylethanoyl)amino]-5-[(3S)-2-oxopyrrolidin-3-yl]pent-2-enoate	2.70 Å	2D2D	2D2D	2D2D	2D2D	2D2D	2D2D	Yang et al., 2005
porcine transmissible gastroenteritis virus-type main peptidase ( transmissible gastroenteritis virus)
complex with an inhibitor N1	2.70 Å	2AMP	2AMP	2AMP	2AMP	2AMP	2AMP	Yang et al., 2005
cruzipain ( Trypanosoma cruzi)
complex with [1-(3-hydroxy-2-oxo-1-phenethyl-propylcarbamoyl)2-phenyl-ethyl]-carbamic acid pyridin-4-ylmethyl ester	1.20 Å	1ME3	1ME3	1ME3	1ME3	1ME3	1ME3	Huang et al., 2003
complex with [1-(1-benzyl-3-hydroxy-2-oxo-propylcarbamoyl)-2-phenyl-ethyl]-carbamic acid benzyl ester	1.20 Å	1ME4	1ME4	1ME4	1ME4	1ME4	1ME4	Huang et al., 2003
RTX self-cleaving toxin ( Vibrio cholerae)
peptidase domain only; complex with Aza-leucine inhibitor	2.35 Å	3GCD	3GCD	3GCD	3GCD	3GCD	3GCD	Shen et al., 2009