deep-principle/science_biology huggingface dataset:
Task: Enzymatic reaction prediction

Reactants (SMILES): CC(C)(CO)C(=O)C(=O)[O-].NC(=O)C1=CN([C@H]2O[C@@H](COP(=O)(O)OP(=O)(O)OC[C@@H]3O[C@H](n4cnc5c(N)ncnc54)[C@@H](OP(=O)(O)O)[C@H]3O)[C@H](O)[C@@H]2O)C=CC1.[H+]
EC Number: 1.1.1.86

Enzyme information:
Accepted name: ketol-acid reductoisomerase (NADP+)
Reaction: (2R)-2,3-dihydroxy-3-methylbutanoate + NADP+ = (2S)-2-hydroxy-2-methyl-3-oxobutanoate + NADPH + H+
Other name(s): dihydroxyisovalerate dehydrogenase (isomerizing); acetohydroxy acid isomeroreductase; ketol acid reductoisomerase; _-keto-_-hydroxylacyl reductoisomerase; 2-hydroxy-3-keto acid reductoisomerase; acetohydroxy acid reductoisomerase; acetolactate reductoisomerase; dihydroxyisovalerate (isomerizing) dehydrogenase; isomeroreductase; reductoisomerase; ketol-acid reductoisomerase; (R)-2,3-dihydroxy-3-methylbutanoate:NADP+ oxidoreductase (isomerizing)
Systematic name: (2R)-2,3-dihydroxy-3-methylbutanoate:NADP+ oxidoreductase (isomerizing)
Comments: Also catalyses the reduction of 2-ethyl-2-hydroxy-3-oxobutanoate to 2,3-dihydroxy-3-methylpentanoate. The enzyme, found in many bacteria and archaea, is specific for NADPH (cf. EC 1.1.1.382, ketol-acid reductoisomerase (NAD+) and EC 1.1.1.383, ketol-acid reductoisomerase [NAD(P)+]).

Instructions: only predict the transformed product of CC(C)(CO)C(=O)C(=O)[O-] in a correct protonation state at the physiological condition.

Predicted product (SMILES): CC(C)(CO)C(O)C(=O)[O-]
Task: Enzymatic reaction prediction

Reactants (SMILES): CC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)COP(=O)([O-])OP(=O)([O-])OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]1OP(=O)([O-])[O-].O=C(O)[C@@H]1CCN1
EC Number: 2.3.1.271

Enzyme information:
Accepted name: L-glutamate 5-semialdehyde N-acetyltransferase
Reaction: acetyl-CoA + L-glutamate 5-semialdehyde = CoA + N-acetyl-L-glutamate 5-semialdehyde
Other name(s): MPR1 (gene name); MPR2 (gene name)
Systematic name: acetyl-CoA:L-glutamate-5-semialdehyde N-acetyltransferase
Comments: The enzyme, characterized from the yeast Saccharomyces cerevisiae Σ1278b, N-acetylates L-glutamate 5-semialdehyde, an L-proline biosynthesis/utilization intermediate, into N-acetyl-L-glutamate 5-semialdehyde, an intermediate of L-arginine biosynthesis, under oxidative stress conditions. Its activity results in conversion of L-proline to L-arginine, and reduction in the concentration of L-glutamate 5-semialdehyde and its equilibrium partner, (S)-1-pyrroline-5-carboxylate, which has been linked to production of reactive oxygen species stress. The enzyme also acts on (S)-1-acetylazetidine-2-carboxylate, a toxic L-proline analog produced by some plants, resulting in its detoxification and conferring resistance on the yeast.

Instructions: only predict the transformed product of O=C(O)[C@@H]1CCN1 in a correct protonation state at the physiological condition.

Predicted product (SMILES): CC(=O)N1CC[C@H]1C(=O)[O-]
Task: Enzymatic reaction prediction

Reactants (SMILES): O.OC[C@H]1O[C@H](O[C@@H]2[C@@H](CO)O[C@H](O[C@@H]3[C@@H](CO)O[C@H](O[C@@H]4[C@@H](CO)O[C@H](O[C@@H]5[C@@H](CO)O[C@H](O[C@@H]6[C@@H](CO)OC(O)[C@H](O)[C@H]6O)[C@H](O)[C@H]5O)[C@H](O)[C@H]4O)[C@H](O)[C@H]3O)[C@H](O)[C@H]2O)[C@H](O)[C@@H](O)[C@@H]1O
EC Number: 3.2.1.1

Enzyme information:
Accepted name: α-amylase
Reaction: Endohydrolysis of (1→4)-α-D-glucosidic linkages in polysaccharides containing three or more (1→4)-α-linked D-glucose units
Other name(s): glycogenase; α-amylase; endoamylase; Taka-amylase A; 1,4-α-D-glucan glucanohydrolase
Systematic name: 4-α-D-glucan glucanohydrolase
Comments: Acts on starch, glycogen and related polysaccharides and oligosaccharides in a random manner; reducing groups are liberated in the α-configuration. The term α relates to the initial anomeric configuration of the free sugar group released and not to the configuration of the linkage hydrolysed.

Instructions: only predict transformed product of OC[C@H]1O[C@H](O[C@@H]2[C@@H](CO)O[C@H](O[C@@H]3[C@@H](CO)O[C@H](O[C@@H]4[C@@H](CO)O[C@H](O[C@@H]5[C@@H](CO)O[C@H](O[C@@H]6[C@@H](CO)OC(O)[C@H](O)[C@H]6O)[C@H](O)[C@H]5O)[C@H](O)[C@H]4O)[C@H](O)[C@H]3O)[C@H](O)[C@H]2O)[C@H](O)[C@@H](O)[C@@H]1O.

Predicted product (SMILES): OC[C@H]1O[C@H](O[C@@H]2[C@@H](CO)O[C@@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@@H](O)[C@@H]1O
Task: Enzymatic reaction prediction

Reactants (SMILES): C[C@H](O)CC(=O)C(=O)[O-]
EC Number: 4.1.3.39

Enzyme information:
Accepted name: 4-hydroxy-2-oxovalerate aldolase
Reaction: (S)-4-hydroxy-2-oxopentanoate = acetaldehyde + pyruvate
Other name(s): 4-hydroxy-2-ketovalerate aldolase; HOA; DmpG; 4-hydroxy-2-oxovalerate pyruvate-lyase; 4-hydroxy-2-oxopentanoate pyruvate-lyase; BphI; 4-hydroxy-2-oxopentanoate pyruvate-lyase (acetaldehyde-forming)
Systematic name: (S)-4-hydroxy-2-oxopentanoate pyruvate-lyase (acetaldehyde-forming)
Comments: Requires Mn2+ for maximal activity. The enzyme from the bacterium Pseudomonas putida is also stimulated by NADH. In some bacterial species the enzyme forms a bifunctional complex with EC 1.2.1.10, acetaldehyde dehydrogenase (acetylating). The enzymes from the bacteria Burkholderia xenovorans and Thermus thermophilus also perform the reaction of EC 4.1.3.43, 4-hydroxy-2-oxohexanoate aldolase.

Instructions: only predict the largest transformed product

Predicted product (SMILES): CC(=O)C(=O)[O-]
Task: Enzymatic reaction prediction

Reactants (SMILES): O=C([O-])[C@@H](O)C(=O)[C@H](O)[C@@H](O)CO
EC Number: 4.1.1.34

Enzyme information:
Accepted name: dehydro-L-gulonate decarboxylase
Reaction: 3-dehydro-L-gulonate = L-xylulose + CO2
Other name(s): keto-L-gulonate decarboxylase; 3-keto-L-gulonate decarboxylase; 3-dehydro-L-gulonate carboxy-lyase
Systematic name: 3-dehydro-L-gulonate carboxy-lyase (L-xylulose-forming)

Instructions: only predict the largest transformed product

Predicted product (SMILES): OCC1(O)OC[C@H](O)[C@H]1O
Task: Enzymatic reaction prediction

Reactants (SMILES): CC(/C=C/C=C(C)/C=C/[C@@]12O[C@]1(C)C[C@@H](O)CC2(C)C)=C\C=C\C=C(C)\C=C\C=C(C)\C=C\[C@@]12O[C@]1(C)C[C@@H](O)CC2(C)C
EC Number: 5.3.99.9

Enzyme information:
Accepted name: neoxanthin synthase
Reaction: violaxanthin = neoxanthin
Other name(s): NSY
Systematic name: violaxanthin-neoxanthin isomerase (epoxide-opening)
Comments: The opening of the epoxide ring of violaxanthin generates a chiral allene. Neoxanthin is a precursor of the plant hormone abscisic acid and the last product of carotenoid synthesis in green plants.

Instructions: nan

Predicted product (SMILES): C/C(C=C=C1C(C)(C)C[C@H](O)C[C@@]1(C)O)=C\C=C\C(C)=C\C=C\C=C(C)\C=C\C=C(C)\C=C\[C@@]12O[C@]1(C)C[C@@H](O)CC2(C)C
Task: Enzymatic reaction prediction

Reactants (SMILES): C[C@]12CC[C@H]3[C@@H](CC=C4CC(O)CC[C@@]43C)[C@@H]1CC[C@@H]2C(=O)CO.NC(=O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)([O-])OP(=O)([O-])OC[C@H]3O[C@@H](n4cnc5c(N)ncnc54)[C@H](OP(=O)([O-])[O-])[C@@H]3O)[C@@H](O)[C@H]2O)c1
EC Number: 5.3.3.1

Enzyme information:
Accepted name: steroid Δ-isomerase
Reaction: A 3-oxo-Δ5-steroid = a 3-oxo-Δ4-steroid
Other name(s): hydroxysteroid isomerase; steroid isomerase; Δ5-ketosteroid isomerase; Δ5(or Δ4)-3-keto steroid isomerase; Δ5-steroid isomerase; 3-oxosteroid isomerase; Δ5-3-keto steroid isomerase; Δ5-3-oxosteroid isomerase
Systematic name: 3-oxosteroid Δ5-Δ4-isomerase
Comments: This activity is catalysed by several distinct enzymes (cf. EC 1.1.3.6, cholesterol oxidase and EC 1.1.1.145, 3-hydroxy-5-steroid dehydrogenase).

Instructions: only predict transformed product of C[C@]12CC[C@H]3[C@@H](CC=C4CC(O)CC[C@@]43C)[C@@H]1CC[C@@H]2C(=O)CO

Predicted product (SMILES): C[C@]12CC[C@H]3[C@@H](CCC4=CC(=O)CC[C@@]43C)[C@@H]1CC[C@@H]2C(=O)CO
Task: Enzymatic reaction prediction

Reactants (SMILES): C[C@H](OP(=O)([O-])OC[C@@H](O)[C@@H](O)[C@@H](O)Cn1c2nc(=O)[n-]c(=O)c-2cc2ccc(O)cc21)C(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)[O-])C(=O)[O-])C(=O)[O-])C(=O)[O-])C(=O)[O-])C(=O)[O-].Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)([O-])OP(=O)([O-])OP(=O)([O-])[O-])[C@@H](O)[C@H]2O)c(=O)[nH]1.[NH3+][C@@H](CCC(=O)[O-])C(=O)[O-]
EC Number: 6.3.2.34

Enzyme information:
Accepted name: coenzyme F420-1:γ-L-glutamate ligase
Reaction: GTP + coenzyme F420-1 + L-glutamate = GDP + phosphate + coenzyme γ-F420-2
Other name(s): F420:γ-glutamyl ligase; CofE-AF; MJ0768; CofE
Systematic name: L-glutamate:coenzyme F420-1 ligase (GDP-forming)
Comments: This protein catalyses the successive addition of two glutamate residues to factor 420 (coenzyme F420) by two distinct and independent reactions. In the first reaction (EC 6.3.2.31, coenzyme F420-0:L-glutamate ligase) the enzyme attaches a glutamate via its α-amine group to F420-0. In the second reaction, which is described here, the enzyme catalyses the addition of a second L-glutamate residue to the γ-carboxyl of the first glutamate.

Instructions: only predict the transformed product of C[C@H](OP(=O)([O-])OC[C@@H](O)[C@@H](O)[C@@H](O)Cn1c2nc(=O)[n-]c(=O)c-2cc2ccc(O)cc21)C(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)[O-])C(=O)[O-])C(=O)[O-])C(=O)[O-])C(=O)[O-])C(=O)[O-] and [NH3+][C@@H](CCC(=O)[O-])C(=O)[O-] in a correct protonation state at the physiological condition.

Predicted product (SMILES): C[C@H](OP(=O)([O-])OC[C@@H](O)[C@@H](O)[C@@H](O)Cn1c2nc(=O)[n-]c(=O)c-2cc2ccc(O)cc21)C(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)[O-])C(=O)[O-])C(=O)[O-])C(=O)[O-])C(=O)[O-])C(=O)[O-])C(=O)[O-]
Task: Enzymatic reaction prediction

Reactants (SMILES): C=C(C)[C@H]1CC=C(C)CC1.NC(=O)C1=CN([C@@H]2O[C@H](COP(=O)([O-])OP(=O)([O-])OC[C@H]3O[C@@H](n4cnc5c(N)ncnc54)[C@H](OP(=O)([O-])[O-])[C@@H]3O)[C@@H](O)[C@H]2O)C=CC1.O=O.[H+]
EC Number: 1.14.14.53

Enzyme information:
Accepted name: (R)-limonene 6-monooxygenase
Reaction: (R)-limonene + [reduced NADPH-hemoprotein reductase] + O2 = (+)-trans-carveol + [oxidized NADPH-hemoprotein reductase] + H2O
Other name(s): (+)-limonene-6-hydroxylase; (+)-limonene 6-monooxygenase
Systematic name: (R)-limonene,[reduced NADPH-hemoprotein reductase]:oxygen oxidoreductase (6-hydroxylating)
Comments: The reaction is stereospecific with over 95% yield of (+)-trans-carveol from (R)-limonene. (S)-Limonene, the substrate for EC 1.14.14.51, (S)-limonene 6-monooxygenase, is not a substrate. Forms part of the carvone biosynthesis pathway in Carum carvi (caraway) seeds.

Instructions: only predict the transformed product of C=C(C)[C@H]1CC=C(C)CC1

Predicted product (SMILES): C=C(C)[C@H]1CC=C(C)[C@H](O)C1
Task: Enzymatic reaction prediction

Reactants (SMILES): CC(C)=CCOP(=O)(O)OP(=O)(O)O.Cc1ccc2[nH]cc(CC(N)C(=O)O)c2c1
EC Number: 2.5.1.80

Enzyme information:
Accepted name: 7-dimethylallyltryptophan synthase
Reaction: dimethylallyl diphosphate + L-tryptophan = diphosphate + 7-(3-methylbut-2-enyl)-L-tryptophan
Other name(s): 7-DMATS
Systematic name: dimethylallyl-diphosphate:L-tryptophan 7-dimethylallyltransferase
Comments: This enzyme is more flexible towards the aromatic substrate than EC 2.5.1.34 (4-dimethylallyltryptophan synthase), but similar to that enzyme, accepts only dimethylallyl diphosphate as the prenyl donor.

Instructions: only predict the transformed product of Cc1ccc2[nH]cc(CC(N)C(=O)O)c2c1

Predicted product (SMILES): CC(C)=CCc1cc(C)cc2c(CC(N)C(=O)O)c[nH]c12
Task: Enzymatic reaction prediction

Reactants (SMILES): C[C@@H]1Nc2nc(N)[nH]c(=O)c2N[C@H]1[C@@H](C)Nc1ccc(C[C@H](O)[C@H](O)[C@H](O)CO[C@H]2O[C@H](COP(=O)([O-])O[C@@H](CCC(=O)[O-])C(=O)N[C@@H](CCC(=O)[O-])C(=O)[O-])[C@@H](O)[C@H]2O)cc1.C[Co+2]
EC Number: 2.1.1.245

Enzyme information:
Accepted name: 5-methyltetrahydrosarcinapterin:corrinoid-iron-sulfur protein Co-methyltransferase
Reaction: a [methyl-Co(III) corrinoid Fe-S protein] + tetrahydrosarcinapterin = a [Co(I) corrinoid Fe-S protein] + 5-methyltetrahydrosarcinapterin
Other name(s): cdhD (gene name); cdhE (gene name)
Systematic name: 5-methyltetrahydrosarcinapterin:corrinoid/iron-sulfur protein methyltransferase
Comments: Catalyses the transfer of a methyl group from the cobamide cofactor of a corrinoid/Fe-S protein to the N5 group of tetrahydrosarcinapterin. Forms, together with EC 1.2.7.4, carbon-monoxide dehydrogenase (ferredoxin) and EC 2.3.1.169, CO-methylating acetyl-CoA synthase, the acetyl-CoA decarbonylase/synthase complex that catalyses the demethylation of acetyl-CoA in a reaction that also forms CO2. This reaction is a key step in methanogenesis from acetate.

Instructions: only predict the transformed product of C[C@@H]1Nc2nc(N)[nH]c(=O)c2N[C@H]1[C@@H](C)Nc1ccc(C[C@H](O)[C@H](O)[C@H](O)CO[C@H]2O[C@H](COP(=O)([O-])O[C@@H](CCC(=O)[O-])C(=O)N[C@@H](CCC(=O)[O-])C(=O)[O-])[C@@H](O)[C@H]2O)cc1 in a correct protonation state at the physiological condition.

Predicted product (SMILES): C[C@@H]1Nc2nc(N)[nH]c(=O)c2N(C)[C@H]1[C@@H](C)Nc1ccc(C[C@H](O)[C@H](O)[C@H](O)CO[C@H]2O[C@H](COP(=O)([O-])O[C@@H](CCC(=O)[O-])C(=O)N[C@@H](CCC(=O)[O-])C(=O)[O-])[C@@H](O)[C@H]2O)cc1
Task: Enzymatic reaction prediction

Reactants (SMILES): CC(=O)O[C@@]12CO[C@@H]1C[C@H](O)[C@@]1(C)C(=O)[C@H](O)C3=C(C)[C@@H](O)C[C@@](O)([C@@H](OC(=O)c4ccccc4)[C@@H]12)C3(C)C.CC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]1OP(=O)(O)O
EC Number: 2.3.1.167

Enzyme information:
Accepted name: 10-deacetylbaccatin III 10-O-acetyltransferase
Reaction: acetyl-CoA + 10-deacetylbaccatin III = CoA + baccatin III
Systematic name: acetyl-CoA:taxan-10β-ol O-acetyltransferase
Comments: The enzyme will not acylate the hydroxy group at 1β, 7β or 13α of 10-deacetyl baccatin III, or at 5α of taxa-4(20),11-dien-5α-ol. May be identical to EC 2.3.1.163, 10-hydroxytaxane O-acetyltransferase.

Instructions: only predict the transformed product of CC(=O)O[C@@]12CO[C@@H]1C[C@H](O)[C@@]1(C)C(=O)[C@H](O)C3=C(C)[C@@H](O)C[C@@](O)([C@@H](OC(=O)c4ccccc4)[C@@H]12)C3(C)C

Predicted product (SMILES): CC(=O)O[C@H]1C(=O)[C@]2(C)[C@@H](O)C[C@H]3OC[C@@]3(OC(C)=O)[C@H]2[C@H](OC(=O)c2ccccc2)[C@]2(O)C[C@H](O)C(C)=C1C2(C)C
Task: Enzymatic reaction prediction

Reactants (SMILES): Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)([O-])OP(=O)([O-])OP(=O)([O-])[O-])[C@@H](O)[C@H]2O)c(=O)[nH]1.O
EC Number: 3.5.4.39

Enzyme information:
Accepted name: GTP cyclohydrolase IV
Reaction: GTP + H2O = 7,8-dihydroneopterin 2',3'-cyclic phosphate + formate + diphosphate
Other name(s): MptA; GTP cyclohydrolase MptA
Systematic name: GTP 7,8-8,9-dihydrolase (cyclizing, formate-releasing, diphosphate-releasing)
Comments: Requires Fe2+. A zinc protein. The enzyme is involved in methanopterin biosynthesis in methanogenic archaea. cf. GTP cyclohydrolase I (EC 3.5.4.16), GTP cyclohydrolase II (EC 3.5.4.25) and GTP cyclohydrolase IIa (EC 3.5.4.29).

Instructions: only predict the largest transformed product

Predicted product (SMILES): Nc1nc2c(c(=O)[nH]1)N=C([C@H](O)[C@H]1COP(=O)([O-])O1)CN2
Task: Enzymatic reaction prediction

Reactants (SMILES): C=C1CC[C@H]2C(C)(C)CCC[C@]2(C)[C@@H]1CC/C(C)=C/COP(=O)([O-])OP(=O)([O-])[O-]
EC Number: 4.2.3.42

Enzyme information:
Accepted name: aphidicolan-16β-ol synthase
Reaction: 9α-copalyl diphosphate + H2O = aphidicolan-16β-ol + diphosphate
Other name(s): PbACS
Systematic name: 9α-copalyl-diphosphate diphosphate-lyase (aphidicolan-16β-ol-forming)
Comment: This is a bifunctional enzyme which also has EC 5.5.1.14 syn-copalyl diphosphate synthase activity. Aphidicolan-16β-ol is a precursor of aphidicolin, a specific inhibitor of DNA polymerase α (EC 2.7.7.7).

Instructions: only predict the largest transformed product

Predicted product (SMILES): CC1(C)CCC[C@@]2(C)[C@H]1CC[C@H]1C[C@H]3C[C@@]12CC[C@@]3(C)O
Task: Enzymatic reaction prediction

Reactants (SMILES): [NH3+][C@@H](Cc1c[nH]cn1)C(=O)[O-]
EC Number: 4.3.1.3

Enzyme information:
Accepted name: histidine ammonia-lyase
Reaction: L-histidine = urocanate + NH3
Other name(s): histidase; histidinase; histidine α-deaminase; L-histidine ammonia-lyase
Systematic name: L-histidine ammonia-lyase (urocanate-forming)
Comments: This enzyme is a member of the aromatic amino acid lyase family, other members of which are EC 4.3.1.23 (tyrosine ammonia-lyase), EC 4.3.1.24 (phenylalanine ammonia-lyase) and EC 4.3.1.25 (phenylalanine/tyrosine ammonia-lyase). The enzyme contains the cofactor 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO), which is common to this family. This unique cofactor is formed autocatalytically by cyclization and dehydration of the three amino-acid residues alanine, serine and glycine. This enzyme catalyses the first step in the degradation of histidine and the product, urocanic acid, is further metabolized to glutamate.

Instructions: only predict the largest transformed product in a correct protonation state at the physiological condition.

Predicted product (SMILES): O=C([O-])/C=C/c1c[nH]cn1
Task: Enzymatic reaction prediction

Reactants (SMILES): O=CC(O)C(O)C(O)CC(=O)[O-]
EC Number: 5.3.1.30

Enzyme information:
Accepted name: 5-deoxy-glucuronate isomerase
Reaction: 5-deoxy-D-glucuronate = 5-dehydro-2-deoxy-D-gluconate
Other name(s): 5DG isomerase; IolB
Systematic name: 5-deoxy-D-glucuronate aldose-ketose-isomerase
Comments: The enzyme, found in the bacterium Bacillus subtilis, is part of a myo-inositol degradation pathway leading to acetyl-CoA.

Instructions: predict the transformed product in a correct protonation state at the physiological condition.

Predicted product (SMILES): O=C([O-])CC(O)C(O)C(=O)CO
Task: Enzymatic reaction prediction

Reactants (SMILES): CC(C)=CCC/C(C)=C/COP(=O)([O-])OP(=O)([O-])[O-]
EC Number: 5.5.1.8

Enzyme information:
Accepted name: (+)-bornyl diphosphate synthase
Reaction: geranyl diphosphate = (+)-bornyl diphosphate
Other name(s): bornyl pyrophosphate synthase (ambiguous); bornyl pyrophosphate synthetase (ambiguous); (+)-bornylpyrophosphate cyclase; geranyl-diphosphate cyclase (ambiguous); (+)-bornyl-diphosphate lyase (decyclizing)
Systematic name: (+)-bornyl-diphosphate lyase (ring-opening)
Comments: Requires Mg2+. The enzyme from Salvia officinalis (sage) can also use (3R)-linalyl diphosphate or more slowly neryl diphosphate in vitro [3]. The reaction proceeds via isomeration of geranyl diphosphate to (3R)-linalyl diphosphate. The oxygen and phosphorus originally linked to C-1 of geranyl diphosphate end up linked to C-2 of (+)-bornyl diphosphate [3]. cf. EC 5.5.1.22 [(-)-bornyl diphosphate synthase].

Instructions: predict the transformed product in a correct protonation state at the physiological condition.

Predicted product (SMILES): CC1(C)C2CCC1(C)[C@@H](OP(=O)([O-])OP(=O)([O-])[O-])C2
Task: Enzymatic reaction prediction

Reactants (SMILES): Cc1cn(C2CC(O)C(COP(=O)(O)OP(=O)(O)OC3OC(C)C(O)C(O)C3O)O2)c(=O)[nH]c1=O
EC Number: 5.4.99.59

Enzyme information:
Accepted name: dTDP-fucopyranose mutase
Reaction: dTDP-α-D-fucopyranose = dTDP-β-D-fucofuranose
Other name(s): Fcf2
Systematic name: dTDP-α-D-fucopyranose furanomutase
Comments: The enzyme is involved in the biosynthesis of the Escherichia coli O52 O antigen.

Instructions: predict the transformed product in a correct protonation state at the physiological condition.

Predicted product (SMILES): Cc1cn(C2CC(O)C(COP(=O)([O-])OP(=O)([O-])OC3OC(C(C)O)C(O)C3O)O2)c(=O)[nH]c1=O
Task: Enzymatic reaction prediction

Reactants (SMILES): C=C1CC23CC1CCC2C12CCCC(C)(C(=O)O1)C2C3C(=O)O.C[S+](CCC(N)C(=O)O)CC1OC(n2cnc3c(N)ncnc32)C(O)C1O
EC Number: 2.1.1.276

Enzyme information:
Accepted name: gibberellin A4 carboxyl methyltransferase
Reaction: S-adenosyl-L-methionine + gibberellin A4 = S-adenosyl-L-homocysteine + methyl gibberellin A4
Other name(s): GAMT2; gibberellin A4 O-methyltransferase
Systematic name: S-adenosyl-L-methionine:gibberellin A4 O-methyltransferase
Comments: The enzyme also methylates gibberellins A34 (80%), A9 (60%), and A3 (45%) with significant activity.

Instructions: predict the transformed product of C=C1CC23CC1CCC2C12CCCC(C)(C(=O)O1)C2C3C(=O)O

Predicted product (SMILES): C=C1CC23CC1CCC2C12CCCC(C)(C(=O)O1)C2C3C(=O)OC
Task: Enzymatic reaction prediction

Reactants (SMILES): CCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)COP(=O)([O-])OP(=O)([O-])OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]1OP(=O)([O-])[O-].C[N+](C)(C)C[C@H](O)CC(=O)[O-]
EC Number: 2.3.1.137

Enzyme information:
Accepted name: carnitine O-octanoyltransferase
Reaction: octanoyl-CoA + L-carnitine = CoA + L-octanoylcarnitine
Other name(s): medium-chain/long-chain carnitine acyltransferase; carnitine medium-chain acyltransferase; easily solubilized mitochondrial carnitine palmitoyltransferase; overt mitochondrial carnitine palmitoyltransferase
Systematic name: octanoyl-CoA:L-carnitine O-octanoyltransferase
Comments: Acts on a range of acyl-CoAs, with optimal activity with C6 or C8 acyl groups. cf. EC 2.3.1.7 (carnitine O-acetyltransferase) and EC 2.3.1.21 (carnitine O-palmitoyltransferase).

Instructions: predict the transformed product of C[N+](C)(C)C[C@H](O)CC(=O)[O-] in a correct protonation state at the physiological condition.

Predicted product (SMILES): CCCCCCCC(=O)O[C@H](CC(=O)[O-])C[N+](C)(C)C