Structure for small-molecule inhibitors of metallopeptidases (unassigned)

Summary Structure

PDB	Organism	Resolution	Comment
1G49	Homo sapiens	1.90 Å	catalytic domain; complex with carboxylic acid based inhibitor (1N)-4-N-butoxyphenylsulfonyl-(2R)-N-hydroxycarboxamido-(4S)-methanesulfonylamino-pyrrolidine
The catalytic and structural zinc ions are shown as light grey CPK spheres. The structural calcium ions are shown as yellow CPK spheres. The zinc ligands are shown in ball-and-stick representation: His218, His222 and His222 in purple. The catalytic Glu219 is shown in blue.

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TERTIARY STRUCTURE DATA
Comment	Resolution	PDB	PDBe	SCOP	CATH	PDBSum	Proteopedia	Reference
anthrax lethal factor ( Bacillus anthracis)
complex with NSC 12155 inhibitor	2.90 Å	1PWP	1PWP	1PWP	1PWP	1PWP	1PWP	Panchal et al., 2004
complex with thioacetyl-Tyr-Pro-Met-NH2 inhibitor	3.52 Å	1PWQ	1PWQ	1PWQ	1PWQ	1PWQ	1PWQ	Turk et al., 2004
complex with (3-(N-hydroxycarboxamido)-2-isobutylpropanoyl-Trp-methylamide inhibitor	2.70 Å	1PWU	1PWU	1PWU	1PWU	1PWU	1PWU	Turk et al., 2004
carboxypeptidase A1 ( Bos taurus)
complex with D-N-hydroxyaminocarbonyl-Phe	2.30 Å	1HDQ	1HDQ	1HDQ	1HDQ	1HDQ	1HDQ	Cho et al., 2002
complex with aminocarbonyl-Phe	1.75 Å	1HDU	1HDU	1HDU	1HDU	1HDU	1HDU	Cho et al., 2002
complex with L-N-hydroxyaminocarbonyl-Phe	1.75 Å	1HEE	1HEE	1HEE	1HEE	1HEE	1HEE	Cho et al., 2002
complex with phenylalanine-N-sulfonamide	2.00 Å	1IY7	1IY7	1IY7	1IY7	1IY7	1IY7	Park et al., 2002
leucyl aminopeptidase 3 ( Bos taurus)
complex with zofenoprilat	1.85 Å	2EWB	2EWB	2EWB	2EWB	2EWB	2EWB	Cappiello et al., 2006
ubiquinol-cytochrome c reductase core protein II ( Bos taurus)
complex with JG144 inhibitor	2.26 Å	2FYU	2FYU	2FYU	2FYU	2FYU	2FYU	Esser et al., 2006
bontoxilysin ( Clostridium botulinum)
complex with bis(5-amidino-benzimidazolyl)methane inhibitor	2.10 Å	1G9A	1G9A	1G9A	1G9A	1G9A	1G9A	Eswaramoorthy et al., 2002
complex with bis(5-amidino-benzimidazolyl)methane inhibitor	2.00 Å	1G9B	1G9B	1G9B	1G9B	1G9B	1G9B	Eswaramoorthy et al., 2002
complex with bis(5-amidino-benzimidazolyl)methane inhibitor	2.35 Å	1G9C	1G9C	1G9C	1G9C	1G9C	1G9C	Eswaramoorthy et al., 2002
complex with bis(5-amidino-benzimidazolyl)methane inhibitor	2.20 Å	1G9D	1G9D	1G9D	1G9D	1G9D	1G9D	Eswaramoorthy et al., 2002
family M27 unassigned peptidases ( Clostridium botulinum)
catalytic domain from serotype A; complex with inhibitory peptide RRGC	1.60 Å	3C88	3C88	3C88	3C88	3C88	3C88
catalytic domain from serotype A; complex with inhibitory peptide RRGM	1.58 Å	3C89	3C89	3C89	3C89	3C89	3C89
peptidyl-dipeptidase Ance ( Drosophila melanogaster)
complex with lisW-S	0.00 Å	2X95	2X95	2X95	2X95	2X95	2X95	Akif et al., 2010
methionyl aminopeptidase 1 (Escherichia-type) ( Escherichia coli)
complex with 5-(2-chlorophenyl)furan-2-carboxylic acid	1.52 Å	1XNZ	1XNZ	1XNZ	1XNZ	1XNZ	1XNZ	Ye et al., 2004
complex with 5-(2-(trifluoromethyl)phenyl)furan-2- carboxylic acid	1.60 Å	2EVC	2EVC	2EVC	2EVC	2EVC	2EVC	Xie et al., 2006
complex with 5-(2,5-dichlorophenyl)furan-2-carboxylic acid	1.70 Å	2EVM	2EVM	2EVM	2EVM	2EVM	2EVM	Xie et al., 2006
complex with n-cyclopentyl-n-(thiazol-2-yl)oxalamide	1.70 Å	2EVO	2EVO	2EVO	2EVO	2EVO	2EVO	Xie et al., 2006
complex with inhibitor YE7	0.00 Å	2P98	2P98	2P98	2P98	2P98	2P98	Huang et al., 2007
complex with inhibitor YE6	0.00 Å	2P99	2P99	2P99	2P99	2P99	2P99	Huang et al., 2007
complex with inhibitor YE6	0.00 Å	2P9A	2P9A	2P9A	2P9A	2P9A	2P9A	Huang et al., 2007
Arg175Gln mutant; complex with amino-hydroxyheptanyl-Ala-Leu-Val-Phe	2.00 Å	3MAT	3MAT	3MAT	3MAT	3MAT	3MAT	Lowther et al., 1999
matrix metallopeptidase-3 ( Homo sapiens)
catalytic domain; complex with diphenylpiperidine sulfonamide inhibitor	2.00 Å	1B8Y	1B8Y	1B8Y	1B8Y	1B8Y	1B8Y	Pavlovsky et al., 1999
complex with N1-hydroxy-2-(3-hydroxy-propyl)-3-isobutyl-N4-[1-(2-methoxy-ethyl)-2-oxo-azepan-3-yl]-succinamide	2.50 Å	1BIW	1BIW	1BIW	1BIW	1BIW	1BIW	Natchus et al., 1998
complex with interstitial collagenase and PG-117025 inhibitor	2.30 Å	1BQO	1BQO	1BQO	1BQO	1BQO	1BQO	Pikul et al., 1998
matrix metallopeptidase-1 ( Homo sapiens)
complex with stromelysin and PG-117025 inhibitor	2.30 Å	1BQO	1BQO	1BQO	1BQO	1BQO	1BQO	Pikul et al., 1998
matrix metallopeptidase-3 ( Homo sapiens)
catalytic domain; complex with diphenyl piperidine sulfonamide	1.80 Å	1CAQ	1CAQ	1CAQ	1CAQ	1CAQ	1CAQ	Pavlovsky et al., 1999
catalytic domain; complex with 3-(1H-indol-3-yl)-2-[4-(4-phenyl-piperidin-1-yl)-benzenesulfonylamino]-propionic acid inhibitor	1.64 Å	1CIZ	1CIZ	1CIZ	1CIZ	1CIZ	1CIZ	Pavlovsky et al., 1999
complex with N-hydroxy-4-[(4-methoxylphenyl)sulfonyl]-2,2-dimethyl-hexahydro-1,4-thiazepine-3(S)-carboxamide	2.60 Å	1D5J	1D5J	1D5J	1D5J	1D5J	1D5J	Almstead et al., 1999
complex with N-hydroxy 1N(4-methoxyphenyl)sulfonyl-4-(Z,E-N-methoxyimino)pyrrolidine-2R-carboxamide inhibitor	2.00 Å	1D7X	1D7X	1D7X	1D7X	1D7X	1D7X	Cheng et al., 1999
complex with N-hydroxy-1-(4-methoxyphenyl)sulfonyl-4-benzyloxycarbonyl-piperazine-2-carboxamide inhibitor	2.40 Å	1D8F	1D8F	1D8F	1D8F	1D8F	1D8F	Cheng et al., 2000
catalytic domain; complex with 1-benzyl-3-(4-methoxy-benzenesulfonyl)-6-oxo-hexahydro-pyrimidine-4-carboxamide inhibitor	2.44 Å	1D8M	1D8M	1D8M	1D8M	1D8M	1D8M	Pikul et al., 2001
catalytic domain; complex with heterocycle-based inhibitor	2.45 Å	1G05	1G05	1G05	1G05	1G05	1G05	Pikul et al., 2001
catalytic domain; complex with carboxylic acid based inhibitor (1N)-4-N-butoxyphenylsulfonyl-(2R)-N-hydroxycarboxamido-(4S)-methanesulfonylamino-pyrrolidine	1.90 Å	1G49	1G49	1G49	1G49	1G49	1G49	Natchus et al., 2000
catalytic domain; complex with HQQ inhibitor	2.00 Å	1G4K	1G4K	1G4K	1G4K	1G4K	1G4K	Dunten et al., 2001
catalytic domain; complex with a carboxylic acid based inhibitor	1.50 Å	1HY7	1HY7	1HY7	1HY7	1HY7	1HY7	Natchus et al., 2001
matrix metallopeptidase-8 ( Homo sapiens)
catalytic domain; complex with 2-(biphenyl-4-sulfonyl)-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid	1.20 Å	1I76	1I76	1I76	1I76	1I76	1I76	Gavuzzo et al., 2000
complex with but-3-enyl-[5-(4-chloro-phenyl)-3,6-dihydro-[1,3,4]thiadiazin-2-ylidene]-amine	2.70 Å	1JH1	1JH1	1JH1	1JH1	1JH1	1JH1	Schroder et al., 2001
matrix metallopeptidase-7 ( Homo sapiens)
complex with 4-methyl-3-(9-oxo-1,8-diaza-tricyclo[10.6.1.0(13,18)]nonadeca-12(19),13(18),15,17-tetraene-10-carbamoyl)penta-methylsulfonediimine	2.30 Å	1MMR	1MMR	1MMR	1MMR	1MMR	1MMR	Browner et al., 1995
matrix metallopeptidase-3 ( Homo sapiens)
catalytic domain; complex with diphenylpiperidine inhibitor	2.00 Å	1QIC	1QIC	1QIC	1QIC	1QIC	1QIC	Pavlovsky et al., 1999
catalytic domain; complex with thiadiazole inhibitor PNU-142372	1.80 Å	1USN	1USN	1USN	1USN	1USN	1USN	Finzel et al., 1998
matrix metallopeptidase-13 ( Homo sapiens)
catalytic domain; complex with pyrimidinetrione inhibitor 5-(2-ethoxyethyl)-5-[4-(4-fluorophenoxy)phenoxy]pyrimidine-2,4,6(1H,3H,5H)-trione	2.30 Å	1YOU	1YOU	1YOU	1YOU	1YOU	1YOU	Blagg et al., 2005
matrix metallopeptidase-8 ( Homo sapiens)
complex with N-2-[(4'-cyano-1,1'-biphenyl-4-yl)oxy]ethyl-N'-hydroxy-N-methylurea	1.80 Å	1ZP5	1ZP5	1ZP5	1ZP5	1ZP5	1ZP5	Campestre et al., 2006
matrix metallopeptidase-13 ( Homo sapiens)
catalytic domain; complex with WAY-033	2.00 Å	1ZTQ	1ZTQ	1ZTQ	1ZTQ	1ZTQ	1ZTQ	Wu et al., 2005
matrix metallopeptidase-12 ( Homo sapiens)
complex with acetohydroxamic acid and (1S,5S,7R)-N~7~-(biphenyl-4-ylmethyl)-N~3~-hydroxy-6,8-dioxa-3-azabicyclo[3.2.1]octane-3,7-dicarboxamide	1.32 Å	2HU6	2HU6	2HU6	2HU6	2HU6	2HU6	Mannino et al., 2006
matrix metallopeptidase-13 ( Homo sapiens)
catalytic domain; complex with benzyl 6-benzyl-5,7-dioxo-6,7-dihydro-5H-[1,3]thiazolo[3,2-C]pyrimidine-2-carboxylate	1.74 Å	2OW9	2OW9	2OW9	2OW9	2OW9	2OW9	Johnson et al., 2007
glutamate carboxypeptidase II ( Homo sapiens)
complex with 2-PMPA (2-phosphonomethyl-pentanedioic acid)	1.71 Å	2PVW	2PVW	2PVW	2PVW	2PVW	2PVW	Barinka et al., 2007
matrix metallopeptidase-3 ( Homo sapiens)
catalytic domain; complex with thiadiazole inhibitor PNU-141803	2.20 Å	2USN	2USN	2USN	2USN	2USN	2USN	Finzel et al., 1998
leukotriene A4 hydrolase ( Homo sapiens)
complex with 2-amino-N-[4-(phenylmethoxy)phenyl]-acetamide	1.80 Å	3CHO	3CHO	3CHO	3CHO	3CHO	3CHO	Kirkland et al., 2008
complex with (3S)-3-amino-4-oxo-4-[(4-phenylmethoxyphenyl) amino]butanoic acid	2.10 Å	3CHP	3CHP	3CHP	3CHP	3CHP	3CHP	Kirkland et al., 2008
complex with N5-[4-(phenylmethoxy)phenyl]-L-glutamine	2.09 Å	3CHQ	3CHQ	3CHQ	3CHQ	3CHQ	3CHQ	Kirkland et al., 2008
complex with 4-amino-N-[4-(phenylmethoxy)phenyl]-butanamide	2.20 Å	3CHR	3CHR	3CHR	3CHR	3CHR	3CHR	Kirkland et al., 2008
complex with (2S)-2-amino-5-[[4-[(2S)-2-hydroxy-2-phenyl- ethoxy]phenyl]amino]-5-oxo-pentanoic acid	2.55 Å	3CHS	3CHS	3CHS	3CHS	3CHS	3CHS	Kirkland et al., 2008
glutamate carboxypeptidase II ( Homo sapiens)
complex with DCFBD inhibitor	1.69 Å	3D7D	3D7D	3D7D	3D7D	3D7D	3D7D	Barinka et al., 2008
complex with DCIT inhibitor	1.54 Å	3D7F	3D7F	3D7F	3D7F	3D7F	3D7F	Barinka et al., 2008
complex with DCMC inhibitor	1.75 Å	3D7G	3D7G	3D7G	3D7G	3D7G	3D7G	Barinka et al., 2008
complex with DCIBZL inhibitor	1.55 Å	3D7H	3D7H	3D7H	3D7H	3D7H	3D7H	Barinka et al., 2008
matrix metallopeptidase-13 ( Homo sapiens)
catalytic domain; complex with 2-4-[4-(4-chloro-phenoxy)-benzenesulfonyl]-tetrahydro-pyran-4-yl-N-hydroxy-acetamide	2.40 Å	456C	456C	456C	456C	456C	456C	Lovejoy et al., 1999
catalytic domain; complex with 4-[4-(4-chloro-phenoxy)-benzenesulfonylmethyl]-tetrahydro-pyran-4-carboxylic acid hydroxyamide	1.60 Å	830C	830C	830C	830C	830C	830C	Lovejoy et al., 1999
matrix metallopeptidase-1 ( Homo sapiens)
catalytic domain; complex with N-hydroxy-2-[4-(4-phenoxy-benzenesulfonyl)-tetrahydro-pyran-4-yl]-acetamide	1.90 Å	966C	966C	966C	966C	966C	966C	Lovejoy et al., 1999