EntityAttribute: Attribute for Catalytic Role, Reactive Part and Reaction State

There are three types in this EntityAttribute, Catalytic Role, Reactive Part, and Reaction State.

EntityAttribute; Catalytic Role

This category of the attribute may be rare, as most of catalytic roles are described in the Reaction Events (EventAttribute).

Ascorbate is a cofactor for myrosinase.
T1 Cofactor 0 9 Ascorbate
T2 Cofactor 15 23 cofactor
T3 Enzyme 28 38 myrosinase
A1 EntityAttribute T2 CatalyticRole
R1 corresponds_to Arg1:T2 Arg2:T1

EntityAttribute; Reactive part

The phrases such as “leaving group”, “acceptor group”, “scissile bond” and “cleavage bond”, which generally describe reactive parts of compounds or enzyme functional groups, will be annotated in this category. Occasionally, the words “group”, “moiety” or “bond” can be abbreviated in these phrases.

general acid catalysis for protonation of the leaving 3'-O anion
T1 Protonation 0 23 general acid catalysis
T2 Protonation 27 38 protonation
T3 EntityProperty 46 53 leaving
T4 FunctionalGroup 54 64 3'-O anion
E1 Protonation:T1 Theme:T4
E2 Protonation:T2 Theme:T4
A1 EntityAttribute T3 ReactivePart
R1 corresponds_to Arg1:T3 Arg2:T4
R2 coreference Arg1:T2 Arg2:T1

the nucleophilic attack of hydroxide ion on the scissile phosphate
T1 NucleophilicAttack 4 23 nucleophilic attack
T2 FunctionalGroup 27 40 hydroxide ion
T3 EntityProperty 48 56 scissile
T4 FunctionalGroup 57 66 phosphate
E1 NucleophilicAttack:T1 Agent:T2 Theme:T4
A1 EntityAttribute T3 ReactivePart
R1 corresponds_to Arg1:T3 Arg2:T4

the proton for donation to the leaving group.
T1 FunctionalGroup 4 10 proton
T2 Protonation 4 23 proton for donation
T3 EntityProperty 31 44 leaving group
E1 Protonation:T2 Theme:T3
A1 EntityAttribute T3 ReactivePart

EntityAttribute; Reaction state

“Substrate(s)”, “product(s)”, “intermediate(s)”, and “transition state(s)”, which are reaction states, will be annotated in this category. In addition, their EntityAttribute will be identified as ReactionState. Those words, which describe the characteristics of these reaction states, such as “covalent”, “tetrahedral”, and “negatively-charged”, will be included in the annotation.

covalent intermediate
T1 EntityProperty 0 21 covalent intermediate
A1 EntityAttribute T1 ReactionState

Moreover, if the functional groups or “enzyme” are indicated adjacent to these words, these functional groups or “enzyme” must be included into the reaction states. Such functional groups or “enzyme” must be connected by “whole_part” relations with the words indicating “Reaction States”, described below in the section of “Relations”.

an acyl enzyme intermediate
T1 FunctionalGroup 3 7 acyl
T2 Enzyme 8 14 enzyme
T3 EntityProperty 3 27 acyl enzyme intermediate
A1 EntityAttribute T3 ReactionState
R1 whole_part Arg1:T3 Arg2:T1
R2 whole_part Arg1:T3 Arg2:T2

The dienol substrate
T1 FunctionalGroup 4 10 dienol
T2 EntityProperty 4 20 dienol substrate
A1 EntityAttribute T2 ReactionState
R1 whole_part Arg1:T2 Arg2:T1

A gem-diol intermediate
T1 FunctionalGroup 2 10 gem-diol
T2 EntityProperty 2 23 gem-diol intermediate
A1 EntityAttribute T2 ReactionState
R1 whole_part Arg1:T2 Arg2:T1

On the other hand, if the independent “compounds” are indicated adjacent to these words, such compounds are not included in the annotation. In that case, the compounds must be connected by “correspond_to” relations with the words indicating “Reaction States”, described below in the section of “Relations”.

histone substrate
T1 OtherCompound 0 7 histone
T2 EntityProperty 8 17 substrate
A1 EntityAttribute T2 ReactionState
R1 corresponds_to Arg1:T2 Arg2:T1

Furthermore, “complexes” of enzyme structures with their corresponding ligand will be annotated in this category, with their “EntityAttribute” identified as “ReactionState”. If the enzyme and its ligand molecules are indicated along with “complex”, the “enzyme” and “ligand molecules” will be included along with “complex” in the annotation, and the relationships will be annotated with “whole_part” from “complex” to “enzyme” or “ligand”, described below in the section of “Relations”.

the complex between adenylate kinase and the inhibitor Ap5A
T1 EntityProperty 4 11 complex
T2 Enzyme 20 36 adenylate kinase
T3 OtherCompound 45 54 inhibitor
T4 OtherCompound 55 59 Ap5A
T5 Inactivation 45 54 inhibitor
E1 Inactivation:T5 Agent:T4 Theme:T2
A1 EntityAttribute T1 ReactionState
R1 whole_part Arg1:T1 Arg2:T2
R2 whole_part Arg1:T1 Arg2:T4
R3 cataphora Arg1:T3 Arg2:T4

the enzyme-substrate complex
T1 Enzyme 4 10 enzyme
T2 EntityProperty 11 20 substrate
T3 EntityProperty 4 28 enzyme-substrate complex
A1 EntityAttribute T2 ReactionState
A2 EntityAttribute T3 ReactionState
R1 whole_part Arg1:T3 Arg2:T1
R2 whole_part Arg1:T3 Arg2:T2