data_XJ0
#
_chem_comp.id XJ0
_chem_comp.name "(E)-3-(2-AMINO-PYRIDINE-5YL)-ACRYLIC ACID"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C7 H7 N3 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "(2E)-3-(2-AMINOPYRIMIDIN-5-YL)PROP-2-ENOIC ACID"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2010-07-01
_chem_comp.pdbx_modified_date 2020-06-17
_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 165.149
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code XJ0
_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 2XJ0
_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
XJ0 OB OB O 0 1 N N N N N N -20.694 -30.691 0.549 3.691 -1.064 0.001 OB XJ0 1
XJ0 C C C 0 1 N N N N N N -21.106 -31.706 1.152 3.304 0.089 0.001 C XJ0 2
XJ0 OA OA O 0 1 N N N N N N -21.304 -31.757 2.386 4.196 1.100 -0.004 OA XJ0 3
XJ0 CA CA C 0 1 N N N N N N -21.360 -32.847 0.400 1.914 0.369 0.001 CA XJ0 4
XJ0 CB CB C 0 1 N N N N N N -21.824 -34.002 1.019 1.020 -0.644 0.000 CB XJ0 5
XJ0 CG CG C 0 1 Y N N N N N -22.093 -35.170 0.312 -0.420 -0.353 -0.000 CG XJ0 6
XJ0 CD CD C 0 1 Y N N N N N -21.916 -35.260 -1.065 -1.365 -1.391 -0.001 CD XJ0 7
XJ0 NE NE N 0 1 Y N N N N N -22.185 -36.393 -1.690 -2.649 -1.086 -0.001 NE XJ0 8
XJ0 CZ CZ C 0 1 Y N N N N N -22.633 -37.465 -1.018 -3.049 0.179 -0.001 CZ XJ0 9
XJ0 NH2 NH2 N 0 1 N N N N N N -22.902 -38.590 -1.674 -4.402 0.452 -0.002 NH2 XJ0 10
XJ0 NH1 NH1 N 0 1 Y N N N N N -22.812 -37.404 0.310 -2.189 1.189 -0.000 NH1 XJ0 11
XJ0 C10 C10 C 0 1 Y N N N N N -22.555 -36.296 0.983 -0.888 0.971 0.006 C10 XJ0 12
XJ0 HA HA H 0 1 N N N N N N -21.094 -30.917 2.776 5.119 0.811 -0.007 HA XJ0 13
XJ0 HB HB H 0 1 N N N N N N -21.197 -32.836 -0.668 1.570 1.393 0.001 HB XJ0 14
XJ0 HC HC H 0 1 N N N N N N -21.981 -33.992 2.087 1.365 -1.667 0.000 HC XJ0 15
XJ0 HD HD H 0 1 N N N N N N -21.560 -34.406 -1.622 -1.046 -2.422 -0.001 HD XJ0 16
XJ0 H10 H10 H 0 1 N N N N N N -22.704 -36.266 2.052 -0.193 1.798 0.011 H10 XJ0 17
XJ0 HH21 HH21 H 0 0 N N N N N N -22.970 -38.398 -2.653 -5.044 -0.275 -0.002 HH21 XJ0 18
XJ0 HH22 HH22 H 0 0 N N N N N N -22.170 -39.252 -1.514 -4.711 1.371 -0.002 HH22 XJ0 19
#
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
XJ0 OB C DOUB N N 1
XJ0 C OA SING N N 2
XJ0 C CA SING N N 3
XJ0 CA CB DOUB N N 4
XJ0 CB CG SING N E 5
XJ0 CG CD SING Y N 6
XJ0 CG C10 DOUB Y N 7
XJ0 CD NE DOUB Y N 8
XJ0 NE CZ SING Y N 9
XJ0 CZ NH2 SING N N 10
XJ0 CZ NH1 DOUB Y N 11
XJ0 NH1 C10 SING Y N 12
XJ0 OA HA SING N N 13
XJ0 CA HB SING N N 14
XJ0 CB HC SING N N 15
XJ0 CD HD SING N N 16
XJ0 C10 H10 SING N N 17
XJ0 NH2 HH21 SING N N 18
XJ0 NH2 HH22 SING N N 19
#
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
XJ0 SMILES ACDLabs 10.04 O=C(O)/C=C/c1cnc(nc1)N
XJ0 SMILES_CANONICAL CACTVS 3.352 Nc1ncc(/C=C/C(O)=O)cn1
XJ0 SMILES CACTVS 3.352 Nc1ncc(C=CC(O)=O)cn1
XJ0 SMILES_CANONICAL "OpenEye OEToolkits" 1.6.1 c1c(cnc(n1)N)\C=C\C(=O)O
XJ0 SMILES "OpenEye OEToolkits" 1.6.1 c1c(cnc(n1)N)C=CC(=O)O
XJ0 InChI InChI 1.03 InChI=1S/C7H7N3O2/c8-7-9-3-5(4-10-7)1-2-6(11)12/h1-4H,(H,11,12)(H2,8,9,10)/b2-1+
XJ0 InChIKey InChI 1.03 ZSTSKJFUYGWSPO-OWOJBTEDSA-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
XJ0 "SYSTEMATIC NAME" ACDLabs 10.04 "(2E)-3-(2-aminopyrimidin-5-yl)prop-2-enoic acid"
XJ0 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "(E)-3-(2-aminopyrimidin-5-yl)prop-2-enoic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
XJ0 'Create component' 2010-07-01 EBI
XJ0 'Modify aromatic_flag' 2011-06-04 RCSB
XJ0 'Modify descriptor' 2011-06-04 RCSB
XJ0 'Modify synonyms' 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id XJ0
_pdbx_chem_comp_synonyms.name "(2E)-3-(2-AMINOPYRIMIDIN-5-YL)PROP-2-ENOIC ACID"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id XJ0
_pdbe_chem_comp_synonyms.name '(2E)-3-(2-AMINOPYRIMIDIN-5-YL)PROP-2-ENOIC ACID'
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
XJ0 OB O 4.299 3.607 1
XJ0 C C 4.299 2.107 2
XJ0 OA O 3.000 1.357 3
XJ0 CA C 5.598 1.357 4
XJ0 CB C 5.598 -0.142 5
XJ0 CG C 6.897 -0.892 6
XJ0 CD C 6.897 -2.393 7
XJ0 NE N 8.196 -3.143 8
XJ0 CZ C 9.495 -2.393 9
XJ0 NH2 N 10.794 -3.143 10
XJ0 NH1 N 9.495 -0.892 11
XJ0 C10 C 8.196 -0.142 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
XJ0 OB C DOUBLE NONE 1
XJ0 C OA SINGLE NONE 2
XJ0 C CA SINGLE ENDUPRIGHT 3
XJ0 CA CB DOUBLE NONE 4
XJ0 CB CG SINGLE ENDUPRIGHT 5
XJ0 CG CD DOUBLE NONE 6
XJ0 CG C10 SINGLE NONE 7
XJ0 CD NE SINGLE NONE 8
XJ0 NE CZ DOUBLE NONE 9
XJ0 CZ NH2 SINGLE NONE 10
XJ0 CZ NH1 SINGLE NONE 11
XJ0 NH1 C10 DOUBLE NONE 12
#
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
XJ0 MurckoScaffold S1 scaffold c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
XJ0 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
XJ0 CG S1 1
XJ0 CD S1 1
XJ0 NE S1 1
XJ0 CZ S1 1
XJ0 NH1 S1 1
XJ0 C10 S1 1
XJ0 CG F1 1
XJ0 CD F1 1
XJ0 NE F1 1
XJ0 CZ F1 1
XJ0 NH1 F1 1
XJ0 C10 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id XJ0
_pdbe_chem_comp_rdkit_properties.exactmw 165.054
_pdbe_chem_comp_rdkit_properties.amw 165.152
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 19
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_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 78.609
_pdbe_chem_comp_rdkit_properties.tpsa 89.100
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.279
_pdbe_chem_comp_rdkit_properties.CrippenMR 42.024
_pdbe_chem_comp_rdkit_properties.chi0v 5.658
_pdbe_chem_comp_rdkit_properties.chi1v 2.776
_pdbe_chem_comp_rdkit_properties.chi2v 0.825
_pdbe_chem_comp_rdkit_properties.chi3v 0.825
_pdbe_chem_comp_rdkit_properties.chi4v 0.431
_pdbe_chem_comp_rdkit_properties.chi0n 12.658
_pdbe_chem_comp_rdkit_properties.chi1n 6.079
_pdbe_chem_comp_rdkit_properties.chi2n 0.825
_pdbe_chem_comp_rdkit_properties.chi3n 0.825
_pdbe_chem_comp_rdkit_properties.chi4n 0.431
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.910
_pdbe_chem_comp_rdkit_properties.kappa1 2.855
_pdbe_chem_comp_rdkit_properties.kappa2 3.472
_pdbe_chem_comp_rdkit_properties.kappa3 2.373
_pdbe_chem_comp_rdkit_properties.Phi 0.826
#
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
XJ0 UniChem ZINC ZINC000014608604
XJ0 UniChem SureChEMBL SCHEMBL1093070
XJ0 UniChem ChemicalBook CB7774773
XJ0 UniChem 'EPA CompTox Dashboard' DTXSID00451634
XJ0 UniChem 'PubChem TPHARMA' 16069063
XJ0 UniChem PubChem 11008273
#
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
XJ0 OB 4.342 1.565 -0.169 ETKDGv3 1
XJ0 C 3.607 0.554 -0.014 ETKDGv3 2
XJ0 OA 4.187 -0.685 0.253 ETKDGv3 3
XJ0 CA 2.147 0.698 -0.121 ETKDGv3 4
XJ0 CB 1.318 -0.340 0.054 ETKDGv3 5
XJ0 CG -0.159 -0.235 -0.038 ETKDGv3 6
XJ0 CD -0.924 -1.222 0.455 ETKDGv3 7
XJ0 NE -2.356 -1.141 0.374 ETKDGv3 8
XJ0 CZ -2.940 -0.123 -0.187 ETKDGv3 9
XJ0 NH2 -4.362 -0.063 -0.255 ETKDGv3 10
XJ0 NH1 -2.149 0.938 -0.744 ETKDGv3 11
XJ0 C10 -0.850 0.909 -0.687 ETKDGv3 12
XJ0 HA 5.192 -0.783 0.326 ETKDGv3 13
XJ0 HB 1.761 1.686 -0.325 ETKDGv3 14
XJ0 HC 1.737 -1.307 0.307 ETKDGv3 15
XJ0 HD -0.476 -2.087 0.930 ETKDGv3 16
XJ0 H10 -0.296 1.716 -1.141 ETKDGv3 17
XJ0 HH21 -4.833 0.752 -0.707 ETKDGv3 18
XJ0 HH22 -4.946 -0.831 0.145 ETKDGv3 19
#