data_LGA
#
_chem_comp.id LGA
_chem_comp.name PYRIMIDIN-2-AMINE
_chem_comp.type non-polymer
_chem_comp.pdbx_type ?
_chem_comp.formula "C4 H5 N3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2008-03-31
_chem_comp.pdbx_modified_date 2011-06-04
_chem_comp.pdbx_ambiguous_flag ?
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 95.103
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code LGA
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 2JJC
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
LGA N2 N2 N 0 1 N N N N N N 61.824 33.405 26.112 61.824 33.405 26.112 N2 LGA 1
LGA C1 C1 C 0 1 Y N N N N N 62.829 33.829 25.352 62.829 33.829 25.352 C1 LGA 2
LGA N1 N1 N 0 1 Y N N N N N 64.085 33.668 25.836 64.085 33.668 25.836 N1 LGA 3
LGA C4 C4 C 0 1 Y N N N N N 65.074 34.109 25.055 65.074 34.109 25.055 C4 LGA 4
LGA C5 C5 C 0 1 Y N N N N N 64.836 34.697 23.837 64.836 34.697 23.837 C5 LGA 5
LGA C3 C3 C 0 1 Y N N N N N 63.533 34.821 23.417 63.533 34.821 23.417 C3 LGA 6
LGA N7 N7 N 0 1 Y N N N N N 62.510 34.385 24.149 62.510 34.385 24.149 N7 LGA 7
LGA H2N1 1H2N H 0 0 N N N N N N 62.140 33.299 27.055 62.140 33.299 27.055 H2N1 LGA 8
LGA H2N2 2H2N H 0 0 N N N N N N 61.080 34.073 26.084 61.080 34.073 26.083 H2N2 LGA 9
LGA H4 H4 H 0 1 N N N N N N 66.094 34.000 25.392 66.094 34.000 25.392 H4 LGA 10
LGA H5 H5 H 0 1 N N N N N N 65.652 35.053 23.225 65.651 35.053 23.225 H5 LGA 11
LGA H3 H3 H 0 1 N N N N N N 63.333 35.287 22.463 63.333 35.287 22.463 H3 LGA 12
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
LGA N2 C1 SING N N 1
LGA C1 N1 SING Y N 2
LGA C1 N7 DOUB Y N 3
LGA N1 C4 DOUB Y N 4
LGA C4 C5 SING Y N 5
LGA C5 C3 DOUB Y N 6
LGA C3 N7 SING Y N 7
LGA N2 H2N1 SING N N 8
LGA N2 H2N2 SING N N 9
LGA C4 H4 SING N N 10
LGA C5 H5 SING N N 11
LGA C3 H3 SING N N 12
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
LGA SMILES ACDLabs 10.04 n1cccnc1N
LGA SMILES_CANONICAL CACTVS 3.341 Nc1ncccn1
LGA SMILES CACTVS 3.341 Nc1ncccn1
LGA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1cnc(nc1)N
LGA SMILES "OpenEye OEToolkits" 1.5.0 c1cnc(nc1)N
LGA InChI InChI 1.03 InChI=1S/C4H5N3/c5-4-6-2-1-3-7-4/h1-3H,(H2,5,6,7)
LGA InChIKey InChI 1.03 LJXQPZWIHJMPQQ-UHFFFAOYSA-N
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
LGA "SYSTEMATIC NAME" ACDLabs 10.04 pyrimidin-2-amine
LGA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 pyrimidin-2-amine
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
LGA 'Create component' 2008-03-31 EBI
LGA 'Modify aromatic_flag' 2011-06-04 RCSB
LGA 'Modify descriptor' 2011-06-04 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
LGA N2 N 6.897 -1.035 1
LGA C1 C 5.598 -0.285 2
LGA N1 N 4.299 -1.035 3
LGA C4 C 3.000 -0.285 4
LGA C5 C 3.000 1.215 5
LGA C3 C 4.299 1.965 6
LGA N7 N 5.598 1.215 7
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
LGA N2 C1 SINGLE NONE 1
LGA C1 N1 DOUBLE NONE 2
LGA C1 N7 SINGLE NONE 3
LGA N1 C4 SINGLE NONE 4
LGA C4 C5 DOUBLE NONE 5
LGA C5 C3 SINGLE NONE 6
LGA C3 N7 DOUBLE NONE 7
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
LGA MurckoScaffold S1 scaffold c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
LGA pyrimidine F1 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
LGA C1 S1 1
LGA N1 S1 1
LGA C4 S1 1
LGA C5 S1 1
LGA C3 S1 1
LGA N7 S1 1
LGA C5 F1 1
LGA C4 F1 1
LGA N1 F1 1
LGA C1 F1 1
LGA N7 F1 1
LGA C3 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id LGA
_pdbe_chem_comp_rdkit_properties.exactmw 95.048
_pdbe_chem_comp_rdkit_properties.amw 95.105
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 7
_pdbe_chem_comp_rdkit_properties.NumAtoms 12
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 48.352
_pdbe_chem_comp_rdkit_properties.tpsa 51.800
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.322
_pdbe_chem_comp_rdkit_properties.CrippenMR 25.620
_pdbe_chem_comp_rdkit_properties.chi0v 3.342
_pdbe_chem_comp_rdkit_properties.chi1v 1.618
_pdbe_chem_comp_rdkit_properties.chi2v 0.424
_pdbe_chem_comp_rdkit_properties.chi3v 0.424
_pdbe_chem_comp_rdkit_properties.chi4v 0.206
_pdbe_chem_comp_rdkit_properties.chi0n 8.342
_pdbe_chem_comp_rdkit_properties.chi1n 4.012
_pdbe_chem_comp_rdkit_properties.chi2n 0.424
_pdbe_chem_comp_rdkit_properties.chi3n 0.424
_pdbe_chem_comp_rdkit_properties.chi4n 0.206
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.120
_pdbe_chem_comp_rdkit_properties.kappa1 1.183
_pdbe_chem_comp_rdkit_properties.kappa2 1.552
_pdbe_chem_comp_rdkit_properties.kappa3 0.855
_pdbe_chem_comp_rdkit_properties.Phi 0.262
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
LGA UniChem ChEBI 38618
LGA UniChem ZINC ZINC000000967472
LGA UniChem fdasrs OB8I17P2G4
LGA UniChem HMDB HMDB0245027
LGA UniChem 'PubChem TPHARMA' 15194230
LGA UniChem PubChem 7978
LGA UniChem ACTor 109-12-6
LGA UniChem ACTor 27043-39-6
LGA UniChem BindingDb 50354823
LGA UniChem 'EPA CompTox Dashboard' DTXSID70870459
LGA UniChem ChemicalBook CB5378100
LGA UniChem CCDC AMPYRM
LGA UniChem Nikkaji J2.875D
LGA UniChem eMolecules 477201
LGA UniChem SureChEMBL SCHEMBL27136
LGA UniChem 'PubChem TPHARMA' 16410323
LGA UniChem Mcule MCULE-4785409568
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
LGA N2 2.413 -0.182 -0.057 ETKDGv3 1
LGA C1 0.993 -0.059 -0.016 ETKDGv3 2
LGA N1 0.444 0.991 0.524 ETKDGv3 3
LGA C4 -0.985 1.134 0.576 ETKDGv3 4
LGA C5 -1.768 0.179 0.066 ETKDGv3 5
LGA C3 -1.132 -1.002 -0.541 ETKDGv3 6
LGA N7 0.166 -1.097 -0.570 ETKDGv3 7
LGA H2N1 2.855 -1.023 -0.489 ETKDGv3 8
LGA H2N2 3.023 0.566 0.342 ETKDGv3 9
LGA H4 -1.422 2.014 1.029 ETKDGv3 10
LGA H5 -2.846 0.271 0.097 ETKDGv3 11
LGA H3 -1.740 -1.791 -0.962 ETKDGv3 12
#