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Literature summary for 3.4.24.B4 extracted from

  • Taylor, S.J.; Abeywardane, A.; Liang, S.; Muegge, I.; Padyana, A.K.; Xiong, Z.; Hill-Drzewi, M.; Farmer, B.; Li, X.; Collins, B.; Li, J.X.; Heim-Riether, A.; Proudfoot, J.; Zhang, Q.; Goldberg, D.; Zuvela-Jelaska, L.; Zaher, H.; Li, J.; Farrow, N.A.
    Fragment-based discovery of indole inhibitors of matrix metalloproteinase-13 (2011), J. Med. Chem., 54, 8174-8187.
    View publication on PubMed
Search for more literature for 3.4.24.B4

Cloned(Commentary)

Cloned (Comment) Organism
a fragment of human MMP-13 corresponding to residues 104-274 is expressed in Escherichia coli BL21(DE3) cells Homo sapiens

Crystallization (Commentary)

Crystallization (Comment) Organism
hanging drop vapor diffusion method, using 10% (w/v) PEG4000, 1 M ammonium formate, and 100 mM Tris, pH 8.0 Homo sapiens

Inhibitors

Inhibitors Comment Organism Structure
(4-[[([5-[2-(ethoxycarbonyl)-1H-indol-5-yl]-1-methyl-1H-pyrazol-3-yl]carbonyl)amino]methyl]phenyl)acetic acid
-
 Homo sapiens
2-butanoyl-1H-indole-5-carboxamide
-
 Homo sapiens
4-[([[5-(1H-indol-5-yl)-1-methyl-1H-pyrazol-3-yl]carbonyl]amino)methyl]benzoic acid
-
 Homo sapiens
4-[[([5-[2-(ethoxycarbonyl)-1H-indol-5-yl]-1-methyl-1H-pyrazol-3-yl]carbonyl)amino]methyl]benzoic acid
-
 Homo sapiens
4-[[([5-[2-(ethoxymethyl)-1H-indol-5-yl]-1-methyl-1H-pyrazol-3-yl]carbonyl)amino]methyl]benzoic acid
-
 Homo sapiens
5-[3-[(4-carboxybenzyl)carbamoyl]-1-methyl-1H-pyrazol-5-yl]-1H-indole-2-carboxylic acid
-
 Homo sapiens
ethyl 5-(1-methyl-1H-imidazol-5-yl)-1H-indole-2-carboxylate
-
 Homo sapiens
ethyl 5-(1-methyl-3-[[(6-oxo-1,6-dihydropyridin-3-yl)methyl]carbamoyl]-1H-pyrazol-5-yl)-1H-indole-2-carboxylate
-
 Homo sapiens
ethyl 5-(3-methylpyridin-4-yl)-1H-indole-2-carboxylate
-
 Homo sapiens
ethyl 5-(acetylamino)-1H-indole-2-carboxylate
-
 Homo sapiens
ethyl 5-(pyridin-2-yl)-1H-indole-2-carboxylate
-
 Homo sapiens
ethyl 5-(pyridin-3-yl)-1H-indole-2-carboxylate
-
 Homo sapiens
ethyl 5-(pyridin-4-yl)-1H-indole-2-carboxylate
-
 Homo sapiens
ethyl 5-carbamoyl-1H-indole-2-carboxylate
-
 Homo sapiens
ethyl 5-phenyl-1H-indole-2-carboxylate
-
 Homo sapiens
ethyl 5-[(methylsulfonyl)amino]-1H-indole-2-carboxylate
-
 Homo sapiens
ethyl 5-[1-methyl-3-[(pyridin-4-ylmethyl)carbamoyl]-1H-pyrazol-5-yl]-1H-indole-2-carboxylate
-
 Homo sapiens
ethyl 5-[3-(methoxycarbonyl)-1-methyl-1H-pyrazol-5-yl]-1H-indole-2-carboxylate
-
 Homo sapiens
ethyl 5-[5-methyl-2-[(pyridin-4-ylmethyl)carbamoyl]pyridin-4-yl]-1H-indole-2-carboxylate
-
 Homo sapiens
N-[2-(4,5-dihydro-1,3-oxazol-2-yl)-1H-indol-5-yl]acetamide
-
 Homo sapiens
N2-ethyl-1H-indole-2,5-dicarboxamide
-
 Homo sapiens

Metals/Ions

Metals/Ions Comment Organism Structure
Ca2+ dependent on Homo sapiens
Zn2+ dependent on Homo sapiens

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
collagen type II + H2O Homo sapiens
-
 ?
-
 ?

Organism

Organism UniProt Comment Textmining
Homo sapiens
-
-
-

Purification (Commentary)

Purification (Comment) Organism
SP Sepharose column chromatography and Superdex 75 gel filtration Homo sapiens

Renatured (Commentary)

Renatured (Comment) Organism
in 50 mM MES, pH 6.5, 500 mM NaCl, 10 mM CaCl2, 1.0 mM ZnCl2, and decreasing concentrations of urea (4-0 M) Homo sapiens

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
collagen type II + H2O
-
 Homo sapiens ?
-
 ?
GABA-Pro-Cha-Abu-Smc-His-Ala-Dab(5-FAM)-Ala-Lys-NH2 + H2O
-
 Homo sapiens ?
-
 ?

Synonyms

Synonyms Comment Organism
MMP-13
-
 Homo sapiens

IC50 Value

IC50 Value IC50 Value Maximum Comment Organism Inhibitor Structure
0.000001
-
 in 100 mM Tris-HCl, pH 7.5, 100 mM NaCl, 10 mM CaCl2, and 0.05% (v/v) Brij 35, and 1% (v/v) DMSO, at 28°C Homo sapiens 4-[[([5-[2-(ethoxycarbonyl)-1H-indol-5-yl]-1-methyl-1H-pyrazol-3-yl]carbonyl)amino]methyl]benzoic acid
0.000003
-
 in 100 mM Tris-HCl, pH 7.5, 100 mM NaCl, 10 mM CaCl2, and 0.05% (v/v) Brij 35, and 1% (v/v) DMSO, at 28°C Homo sapiens (4-[[([5-[2-(ethoxycarbonyl)-1H-indol-5-yl]-1-methyl-1H-pyrazol-3-yl]carbonyl)amino]methyl]phenyl)acetic acid
0.00009
-
 in 100 mM Tris-HCl, pH 7.5, 100 mM NaCl, 10 mM CaCl2, and 0.05% (v/v) Brij 35, and 1% (v/v) DMSO, at 28°C Homo sapiens ethyl 5-[1-methyl-3-[(pyridin-4-ylmethyl)carbamoyl]-1H-pyrazol-5-yl]-1H-indole-2-carboxylate
0.00012
-
 in 100 mM Tris-HCl, pH 7.5, 100 mM NaCl, 10 mM CaCl2, and 0.05% (v/v) Brij 35, and 1% (v/v) DMSO, at 28°C Homo sapiens ethyl 5-(1-methyl-3-[[(6-oxo-1,6-dihydropyridin-3-yl)methyl]carbamoyl]-1H-pyrazol-5-yl)-1H-indole-2-carboxylate
0.00015
-
 in 100 mM Tris-HCl, pH 7.5, 100 mM NaCl, 10 mM CaCl2, and 0.05% (v/v) Brij 35, and 1% (v/v) DMSO, at 28°C Homo sapiens ethyl 5-[5-methyl-2-[(pyridin-4-ylmethyl)carbamoyl]pyridin-4-yl]-1H-indole-2-carboxylate
0.00025
-
 in 100 mM Tris-HCl, pH 7.5, 100 mM NaCl, 10 mM CaCl2, and 0.05% (v/v) Brij 35, and 1% (v/v) DMSO, at 28°C Homo sapiens 4-[[([5-[2-(ethoxymethyl)-1H-indol-5-yl]-1-methyl-1H-pyrazol-3-yl]carbonyl)amino]methyl]benzoic acid
0.0024
-
 in 100 mM Tris-HCl, pH 7.5, 100 mM NaCl, 10 mM CaCl2, and 0.05% (v/v) Brij 35, and 1% (v/v) DMSO, at 28°C Homo sapiens ethyl 5-[3-(methoxycarbonyl)-1-methyl-1H-pyrazol-5-yl]-1H-indole-2-carboxylate
0.0025
-
 in 100 mM Tris-HCl, pH 7.5, 100 mM NaCl, 10 mM CaCl2, and 0.05% (v/v) Brij 35, and 1% (v/v) DMSO, at 28°C Homo sapiens ethyl 5-(1-methyl-1H-imidazol-5-yl)-1H-indole-2-carboxylate
0.0096
-
 in 100 mM Tris-HCl, pH 7.5, 100 mM NaCl, 10 mM CaCl2, and 0.05% (v/v) Brij 35, and 1% (v/v) DMSO, at 28°C Homo sapiens ethyl 5-(3-methylpyridin-4-yl)-1H-indole-2-carboxylate
0.015
-
 in 100 mM Tris-HCl, pH 7.5, 100 mM NaCl, 10 mM CaCl2, and 0.05% (v/v) Brij 35, and 1% (v/v) DMSO, at 28°C Homo sapiens ethyl 5-(pyridin-3-yl)-1H-indole-2-carboxylate
0.025
-
 in 100 mM Tris-HCl, pH 7.5, 100 mM NaCl, 10 mM CaCl2, and 0.05% (v/v) Brij 35, and 1% (v/v) DMSO, at 28°C Homo sapiens 5-[3-[(4-carboxybenzyl)carbamoyl]-1-methyl-1H-pyrazol-5-yl]-1H-indole-2-carboxylic acid
0.026
-
 IC50 above 0.026 mM; in 100 mM Tris-HCl, pH 7.5, 100 mM NaCl, 10 mM CaCl2, and 0.05% (v/v) Brij 35, and 1% (v/v) DMSO, at 28°C Homo sapiens 4-[([[5-(1H-indol-5-yl)-1-methyl-1H-pyrazol-3-yl]carbonyl]amino)methyl]benzoic acid
0.031
-
 in 100 mM Tris-HCl, pH 7.5, 100 mM NaCl, 10 mM CaCl2, and 0.05% (v/v) Brij 35, and 1% (v/v) DMSO, at 28°C Homo sapiens ethyl 5-(acetylamino)-1H-indole-2-carboxylate
0.039
-
 in 100 mM Tris-HCl, pH 7.5, 100 mM NaCl, 10 mM CaCl2, and 0.05% (v/v) Brij 35, and 1% (v/v) DMSO, at 28°C Homo sapiens ethyl 5-carbamoyl-1H-indole-2-carboxylate
0.082
-
 in 100 mM Tris-HCl, pH 7.5, 100 mM NaCl, 10 mM CaCl2, and 0.05% (v/v) Brij 35, and 1% (v/v) DMSO, at 28°C Homo sapiens ethyl 5-(pyridin-4-yl)-1H-indole-2-carboxylate
0.097
-
 in 100 mM Tris-HCl, pH 7.5, 100 mM NaCl, 10 mM CaCl2, and 0.05% (v/v) Brij 35, and 1% (v/v) DMSO, at 28°C Homo sapiens ethyl 5-[(methylsulfonyl)amino]-1H-indole-2-carboxylate
0.22
-
 in 100 mM Tris-HCl, pH 7.5, 100 mM NaCl, 10 mM CaCl2, and 0.05% (v/v) Brij 35, and 1% (v/v) DMSO, at 28°C Homo sapiens N-[2-(4,5-dihydro-1,3-oxazol-2-yl)-1H-indol-5-yl]acetamide
0.5
-
 IC50 above 0.5 mM, in 100 mM Tris-HCl, pH 7.5, 100 mM NaCl, 10 mM CaCl2, and 0.05% (v/v) Brij 35, and 1% (v/v) DMSO, at 28°C Homo sapiens 2-butanoyl-1H-indole-5-carboxamide
0.5
-
 IC50 above 0.5 mM, in 100 mM Tris-HCl, pH 7.5, 100 mM NaCl, 10 mM CaCl2, and 0.05% (v/v) Brij 35, and 1% (v/v) DMSO, at 28°C Homo sapiens N2-ethyl-1H-indole-2,5-dicarboxamide
0.5
-
 IC50 above 0.5 mM, in 100 mM Tris-HCl, pH 7.5, 100 mM NaCl, 10 mM CaCl2, and 0.05% (v/v) Brij 35, and 1% (v/v) DMSO, at 28°C Homo sapiens ethyl 5-phenyl-1H-indole-2-carboxylate
0.5
-
 IC50 above 0.5 mM, in 100 mM Tris-HCl, pH 7.5, 100 mM NaCl, 10 mM CaCl2, and 0.05% (v/v) Brij 35, and 1% (v/v) DMSO, at 28°C Homo sapiens ethyl 5-(pyridin-2-yl)-1H-indole-2-carboxylate