data_T0A
#
_chem_comp.id T0A
_chem_comp.name 5-deazatetrahydropterin
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C7 H10 N4 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2018-12-08
_chem_comp.pdbx_modified_date 2019-12-13
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 166.180
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code T0A
_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 6Q57
_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
T0A NAH N1 N 0 1 N N N N N N -0.722 19.759 -27.142 1.903 -0.747 -0.002 NAH T0A 1
T0A CAL C1 C 0 1 N N N N N N 0.527 19.399 -26.717 0.696 -1.349 -0.033 CAL T0A 2
T0A OAB O1 O 0 1 N N N N N N 1.303 18.690 -27.655 0.610 -2.566 -0.060 OAB T0A 3
T0A CAK C2 C 0 1 N N N N N N 1.068 19.674 -25.461 -0.456 -0.553 -0.033 CAK T0A 4
T0A CAE C3 C 0 1 N N N N N N 2.401 19.282 -25.027 -1.808 -1.211 -0.071 CAE T0A 5
T0A CAC C4 C 0 1 N N N N N N 2.618 19.282 -23.469 -2.885 -0.244 0.425 CAC T0A 6
T0A CAD C5 C 0 1 N N N N N N 1.998 20.570 -22.869 -2.737 1.086 -0.327 CAD T0A 7
T0A NAG N2 N 0 1 N N N N N N 0.589 20.760 -23.282 -1.422 1.649 0.007 NAG T0A 8
T0A CAJ C6 C 0 1 N N N N N N 0.194 20.390 -24.621 -0.315 0.822 -0.002 CAJ T0A 9
T0A NAF N3 N 0 1 N N N N N N -1.069 20.803 -24.953 0.910 1.365 0.022 NAF T0A 10
T0A CAI C7 C 0 1 N N N N N N -1.446 20.455 -26.201 1.989 0.611 0.023 CAI T0A 11
T0A NAA N4 N 0 1 N N N N N N -2.806 20.868 -26.618 3.223 1.205 0.049 NAA T0A 12
T0A H1 H1 H 0 1 N N N N N N -1.076 19.537 -28.051 2.711 -1.283 0.006 H1 T0A 13
T0A H3 H3 H 0 1 N N N N N N 2.596 18.265 -25.399 -2.036 -1.510 -1.094 H3 T0A 14
T0A H4 H4 H 0 1 N N N N N N 3.124 19.981 -25.473 -1.797 -2.096 0.566 H4 T0A 15
T0A H5 H5 H 0 1 N N N N N N 2.130 18.399 -23.029 -3.871 -0.665 0.232 H5 T0A 16
T0A H6 H6 H 0 1 N N N N N N 3.695 19.254 -23.247 -2.759 -0.075 1.494 H6 T0A 17
T0A H7 H7 H 0 1 N N N N N N 2.039 20.505 -21.772 -2.802 0.912 -1.401 H7 T0A 18
T0A H8 H8 H 0 1 N N N N N N 2.586 21.436 -23.207 -3.523 1.774 -0.017 H8 T0A 19
T0A H9 H9 H 0 1 N N N N N N -3.390 21.377 -25.985 4.024 0.659 0.049 H9 T0A 20
T0A H10 H10 H 0 1 N N N N N N -3.140 20.638 -27.532 3.295 2.172 0.067 H10 T0A 21
T0A H2 H2 H 0 1 N N N N N N 0.381 21.732 -23.173 -1.332 2.589 0.230 H2 T0A 22
#
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
T0A OAB CAL DOUB N N 1
T0A NAH CAL SING N N 2
T0A NAH CAI SING N N 3
T0A CAL CAK SING N N 4
T0A NAA CAI SING N N 5
T0A CAI NAF DOUB N N 6
T0A CAK CAE SING N N 7
T0A CAK CAJ DOUB N N 8
T0A CAE CAC SING N N 9
T0A NAF CAJ SING N N 10
T0A CAJ NAG SING N N 11
T0A CAC CAD SING N N 12
T0A NAG CAD SING N N 13
T0A NAH H1 SING N N 14
T0A CAE H3 SING N N 15
T0A CAE H4 SING N N 16
T0A CAC H5 SING N N 17
T0A CAC H6 SING N N 18
T0A CAD H7 SING N N 19
T0A CAD H8 SING N N 20
T0A NAA H9 SING N N 21
T0A NAA H10 SING N N 22
T0A NAG H2 SING N N 23
#
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
T0A InChI InChI 1.03 InChI=1S/C7H10N4O/c8-7-10-5-4(6(12)11-7)2-1-3-9-5/h1-3H2,(H4,8,9,10,11,12)
T0A InChIKey InChI 1.03 PRQFDDYAWVNJMM-UHFFFAOYSA-N
T0A SMILES_CANONICAL CACTVS 3.385 NC1=NC2=C(CCCN2)C(=O)N1
T0A SMILES CACTVS 3.385 NC1=NC2=C(CCCN2)C(=O)N1
T0A SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 C1CC2=C(NC1)N=C(NC2=O)N
T0A SMILES "OpenEye OEToolkits" 2.0.6 C1CC2=C(NC1)N=C(NC2=O)N
#
_pdbx_chem_comp_identifier.comp_id T0A
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.6
_pdbx_chem_comp_identifier.identifier 2-azanyl-5,6,7,8-tetrahydro-3~{H}-pyrido[2,3-d]pyrimidin-4-one
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
T0A 'Create component' 2018-12-08 EBI
T0A 'Initial release' 2019-12-18 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
T0A NAH N 8.298 0.491 1
T0A CAL C 6.999 1.241 2
T0A OAB O 6.999 2.741 3
T0A CAK C 5.700 0.491 4
T0A CAE C 4.359 1.293 5
T0A CAC C 3.000 0.522 6
T0A CAD C 3.000 -1.040 7
T0A NAG N 4.359 -1.811 8
T0A CAJ C 5.700 -1.009 9
T0A NAF N 6.999 -1.759 10
T0A CAI C 8.298 -1.009 11
T0A NAA N 9.597 -1.759 12
#
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
T0A OAB CAL DOUBLE NONE 1
T0A NAH CAL SINGLE NONE 2
T0A NAH CAI SINGLE NONE 3
T0A CAL CAK SINGLE NONE 4
T0A NAA CAI SINGLE NONE 5
T0A CAI NAF DOUBLE NONE 6
T0A CAK CAE SINGLE NONE 7
T0A CAK CAJ DOUBLE NONE 8
T0A CAE CAC SINGLE NONE 9
T0A NAF CAJ SINGLE NONE 10
T0A CAJ NAG SINGLE NONE 11
T0A CAC CAD SINGLE NONE 12
T0A NAG CAD SINGLE NONE 13
#
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
T0A MurckoScaffold S1 scaffold 'O=c1[nH]cnc2c1CCCN2' InChI=1S/C7H9N3O/c11-7-5-2-1-3-8-6(5)9-4-10-7/h4H,1-3H2,(H2,8,9,10,11) YJIRCOHLVHBXAK-UHFFFAOYSA-N
T0A pyrimidine F1 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
T0A Z1139192314 F2 fragment 'O=c1[nH]cnc2c1CCCN2' InChI=1S/C7H9N3O/c11-7-5-2-1-3-8-6(5)9-4-10-7/h4H,1-3H2,(H2,8,9,10,11) YJIRCOHLVHBXAK-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
T0A NAH S1 1
T0A CAL S1 1
T0A OAB S1 1
T0A CAK S1 1
T0A CAE S1 1
T0A CAC S1 1
T0A CAD S1 1
T0A NAG S1 1
T0A CAJ S1 1
T0A NAF S1 1
T0A CAI S1 1
T0A CAK F1 1
T0A CAL F1 1
T0A NAH F1 1
T0A CAI F1 1
T0A NAF F1 1
T0A CAJ F1 1
T0A OAB F2 1
T0A CAL F2 1
T0A NAH F2 1
T0A CAI F2 1
T0A NAF F2 1
T0A CAJ F2 1
T0A NAG F2 1
T0A CAD F2 1
T0A CAC F2 1
T0A CAE F2 1
T0A CAK F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id T0A
_pdbe_chem_comp_rdkit_properties.exactmw 166.085
_pdbe_chem_comp_rdkit_properties.amw 166.184
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 22
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.429
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_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 83.293
_pdbe_chem_comp_rdkit_properties.tpsa 83.800
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.206
_pdbe_chem_comp_rdkit_properties.CrippenMR 44.275
_pdbe_chem_comp_rdkit_properties.chi0v 5.697
_pdbe_chem_comp_rdkit_properties.chi1v 3.019
_pdbe_chem_comp_rdkit_properties.chi2v 1.250
_pdbe_chem_comp_rdkit_properties.chi3v 1.250
_pdbe_chem_comp_rdkit_properties.chi4v 0.780
_pdbe_chem_comp_rdkit_properties.chi0n 15.697
_pdbe_chem_comp_rdkit_properties.chi1n 7.808
_pdbe_chem_comp_rdkit_properties.chi2n 1.250
_pdbe_chem_comp_rdkit_properties.chi3n 1.250
_pdbe_chem_comp_rdkit_properties.chi4n 0.780
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.520
_pdbe_chem_comp_rdkit_properties.kappa1 2.041
_pdbe_chem_comp_rdkit_properties.kappa2 2.510
_pdbe_chem_comp_rdkit_properties.kappa3 1.028
_pdbe_chem_comp_rdkit_properties.Phi 0.427
#
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
T0A UniChem ZINC ZINC000017324969
T0A UniChem SureChEMBL SCHEMBL15757443
T0A UniChem ACTor 6964-95-0
T0A UniChem 'EPA CompTox Dashboard' DTXSID20290148
T0A UniChem PubChem 135460259
#
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
T0A NAH -2.300 1.060 -0.407 ETKDGv3 1
T0A CAL -0.977 1.502 -0.716 ETKDGv3 2
T0A OAB -0.795 2.632 -1.245 ETKDGv3 3
T0A CAK 0.160 0.614 -0.409 ETKDGv3 4
T0A CAE 1.572 1.023 -0.763 ETKDGv3 5
T0A CAC 2.612 0.274 0.079 ETKDGv3 6
T0A CAD 2.348 -1.231 0.028 ETKDGv3 7
T0A NAG 0.967 -1.511 0.414 ETKDGv3 8
T0A CAJ -0.103 -0.602 0.115 ETKDGv3 9
T0A NAF -1.456 -0.997 0.411 ETKDGv3 10
T0A CAI -2.485 -0.236 0.175 ETKDGv3 11
T0A NAA -3.797 -0.697 0.495 ETKDGv3 12
T0A H1 -3.121 1.674 -0.608 ETKDGv3 13
T0A H3 1.746 0.812 -1.840 ETKDGv3 14
T0A H4 1.705 2.114 -0.599 ETKDGv3 15
T0A H5 2.557 0.622 1.133 ETKDGv3 16
T0A H6 3.632 0.488 -0.307 ETKDGv3 17
T0A H7 3.042 -1.755 0.718 ETKDGv3 18
T0A H8 2.522 -1.609 -1.003 ETKDGv3 19
T0A H9 -3.939 -1.641 0.918 ETKDGv3 20
T0A H10 -4.629 -0.095 0.309 ETKDGv3 21
T0A H2 0.741 -2.439 0.839 ETKDGv3 22
#