BRENDA - Enzyme Database

Malonate-based inhibitors of mammalian serine racemase kinetic characterization and structure-based computational study

Vorlova, B.; Nachtigallova, D.; Jiraskova-Vanickova, J.; Ajani, H.; Jansa, P.; Rezac, J.; Fanfrlik, J.; Otyepka, M.; Hobza, P.; Konvalinka, J.; Lepsik, M.; Eur. J. Med. Chem. 89, 189-197 (2015)

Data extracted from this reference:

Activating Compound
EC Number
Activating Compound
Commentary
Organism
Structure
5.1.1.18
ATP
-
Homo sapiens
5.1.1.18
Ca2+
-
Homo sapiens
5.1.1.18
Mg2+
-
Homo sapiens
5.1.1.18
Mn2+
-
Homo sapiens
Inhibitors
EC Number
Inhibitors
Commentary
Organism
Structure
5.1.1.18
(thiophen-3-yl)propanedioate
-
Homo sapiens
5.1.1.18
2,2-dichloromalonate
-
Homo sapiens
5.1.1.18
2,2-difluoromalonate
-
Homo sapiens
5.1.1.18
2-aminomalonate
-
Homo sapiens
5.1.1.18
2-carboxylmalonate
-
Homo sapiens
5.1.1.18
2-chloromalonate
-
Homo sapiens
5.1.1.18
2-fluoromalonate
-
Homo sapiens
5.1.1.18
2-Hydroxymalonate
-
Homo sapiens
5.1.1.18
2-nitromalonate
-
Homo sapiens
5.1.1.18
3-aminopropane-1,1,3-tricarboxylate
-
Homo sapiens
5.1.1.18
benzylpropanedioate
-
Homo sapiens
5.1.1.18
bis(hydroxymethyl)propanedioate
-
Homo sapiens
5.1.1.18
butylpropanedioic acid
-
Homo sapiens
5.1.1.18
cyclobutane-1,1,3,3-tetracarboxylate
-
Homo sapiens
5.1.1.18
dimethylmalonate
-
Homo sapiens
5.1.1.18
ethane-1,1,2,2-tetracarboxylic acid
-
Homo sapiens
5.1.1.18
ethane-1,1,2-tricarboxylate
-
Homo sapiens
5.1.1.18
malonate
-
Homo sapiens
5.1.1.18
methylmalonate
-
Homo sapiens
5.1.1.18
additional information
malonate-based inhibitors of mammalian serine racemase, kinetic characterization and structure-based computational study. Enzyme-inhibitor structure-activity relationship. Ligand docking into the human enzyme active site with three thermodynamically favourable water molecules is able to discern qualitatively between good and weak inhibitors. Further improvement in ranking is obtained using advanced PM6-D3H4X/COSMO semiempirical quantum mechanics-based scoring which distinguishes between the compounds with IC50 better/worse than 2 mM, molecular dynamics, method, overview
Homo sapiens
5.1.1.18
oxirane-2,3-dicarboxylate
-
Homo sapiens
5.1.1.18
propane-1,2,2,3-tetracarboxylate
-
Homo sapiens
Natural Substrates/ Products (Substrates)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
5.1.1.18
L-serine
Homo sapiens
-
D-serine
-
-
r
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
5.1.1.18
Homo sapiens
Q9GZT4
-
-
Source Tissue
EC Number
Source Tissue
Commentary
Organism
Textmining
5.1.1.18
brain
-
Homo sapiens
-
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
5.1.1.18
L-serine
-
747702
Homo sapiens
D-serine
-
-
-
r
Temperature Optimum [°C]
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
5.1.1.18
37
-
assay at
Homo sapiens
pH Optimum
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
5.1.1.18
8
-
assay at
Homo sapiens
Cofactor
EC Number
Cofactor
Commentary
Organism
Structure
5.1.1.18
pyridoxal 5'-phosphate
-
Homo sapiens
Activating Compound (protein specific)
EC Number
Activating Compound
Commentary
Organism
Structure
5.1.1.18
ATP
-
Homo sapiens
5.1.1.18
Ca2+
-
Homo sapiens
5.1.1.18
Mg2+
-
Homo sapiens
5.1.1.18
Mn2+
-
Homo sapiens
Cofactor (protein specific)
EC Number
Cofactor
Commentary
Organism
Structure
5.1.1.18
pyridoxal 5'-phosphate
-
Homo sapiens
Inhibitors (protein specific)
EC Number
Inhibitors
Commentary
Organism
Structure
5.1.1.18
(thiophen-3-yl)propanedioate
-
Homo sapiens
5.1.1.18
2,2-dichloromalonate
-
Homo sapiens
5.1.1.18
2,2-difluoromalonate
-
Homo sapiens
5.1.1.18
2-aminomalonate
-
Homo sapiens
5.1.1.18
2-carboxylmalonate
-
Homo sapiens
5.1.1.18
2-chloromalonate
-
Homo sapiens
5.1.1.18
2-fluoromalonate
-
Homo sapiens
5.1.1.18
2-Hydroxymalonate
-
Homo sapiens
5.1.1.18
2-nitromalonate
-
Homo sapiens
5.1.1.18
3-aminopropane-1,1,3-tricarboxylate
-
Homo sapiens
5.1.1.18
benzylpropanedioate
-
Homo sapiens
5.1.1.18
bis(hydroxymethyl)propanedioate
-
Homo sapiens
5.1.1.18
butylpropanedioic acid
-
Homo sapiens
5.1.1.18
cyclobutane-1,1,3,3-tetracarboxylate
-
Homo sapiens
5.1.1.18
dimethylmalonate
-
Homo sapiens
5.1.1.18
ethane-1,1,2,2-tetracarboxylic acid
-
Homo sapiens
5.1.1.18
ethane-1,1,2-tricarboxylate
-
Homo sapiens
5.1.1.18
malonate
-
Homo sapiens
5.1.1.18
methylmalonate
-
Homo sapiens
5.1.1.18
additional information
malonate-based inhibitors of mammalian serine racemase, kinetic characterization and structure-based computational study. Enzyme-inhibitor structure-activity relationship. Ligand docking into the human enzyme active site with three thermodynamically favourable water molecules is able to discern qualitatively between good and weak inhibitors. Further improvement in ranking is obtained using advanced PM6-D3H4X/COSMO semiempirical quantum mechanics-based scoring which distinguishes between the compounds with IC50 better/worse than 2 mM, molecular dynamics, method, overview
Homo sapiens
5.1.1.18
oxirane-2,3-dicarboxylate
-
Homo sapiens
5.1.1.18
propane-1,2,2,3-tetracarboxylate
-
Homo sapiens
Natural Substrates/ Products (Substrates) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
5.1.1.18
L-serine
Homo sapiens
-
D-serine
-
-
r
Source Tissue (protein specific)
EC Number
Source Tissue
Commentary
Organism
Textmining
5.1.1.18
brain
-
Homo sapiens
-
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
5.1.1.18
L-serine
-
747702
Homo sapiens
D-serine
-
-
-
r
Temperature Optimum [°C] (protein specific)
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
5.1.1.18
37
-
assay at
Homo sapiens
pH Optimum (protein specific)
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
5.1.1.18
8
-
assay at
Homo sapiens