data_HR3
#
_chem_comp.id HR3
_chem_comp.name "5-((4-methoxybenzyl)amino)pyridine-2,4-dicarboxylic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C15 H14 N2 O5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-01-29
_chem_comp.pdbx_modified_date 2022-01-28
_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 302.282
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code HR3
_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 7DYT
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
HR3 C10 C1 C 0 1 Y N N N N N -0.621 10.480 -24.213 5.140 -0.247 0.217 C10 HR3 1
HR3 C13 C2 C 0 1 N N N N N N 1.457 9.529 -23.958 7.118 0.408 -0.928 C13 HR3 2
HR3 C15 C3 C 0 1 N N N N N N -6.353 13.152 -21.502 -1.394 2.280 0.104 C15 HR3 3
HR3 C1 C4 C 0 1 Y N N N N N -6.604 12.090 -23.708 -1.196 -0.221 0.041 C1 HR3 4
HR3 C2 C5 C 0 1 Y N N N N N -7.586 11.573 -24.450 -1.813 -1.474 -0.014 C2 HR3 5
HR3 C3 C6 C 0 1 Y N N N N N -9.268 11.899 -23.162 -3.914 -0.515 -0.054 C3 HR3 6
HR3 C4 C7 C 0 1 Y N N N N N -8.473 12.467 -22.196 -3.387 0.772 -0.002 C4 HR3 7
HR3 C5 C8 C 0 1 Y N N N N N -7.122 12.560 -22.475 -2.000 0.934 0.047 C5 HR3 8
HR3 C6 C9 C 0 1 N N N N N N -4.746 10.908 -24.748 1.011 -1.320 -0.035 C6 HR3 9
HR3 C7 C10 C 0 1 Y N N N N N -3.274 10.763 -24.543 2.466 -0.937 0.054 C7 HR3 10
HR3 C8 C11 C 0 1 Y N N N N N -2.531 11.825 -24.258 3.098 -0.912 1.284 C8 HR3 11
HR3 C9 C12 C 0 1 Y N N N N N -1.235 11.637 -24.106 4.432 -0.562 1.368 C9 HR3 12
HR3 C11 C13 C 0 1 Y N N N N N -1.383 9.421 -24.502 4.504 -0.279 -1.015 C11 HR3 13
HR3 C12 C14 C 0 1 Y N N N N N -2.707 9.522 -24.682 3.169 -0.624 -1.094 C12 HR3 14
HR3 C14 C15 C 0 1 N N N N N N -10.638 11.691 -23.017 -5.379 -0.700 -0.106 C14 HR3 15
HR3 N1 N1 N 0 1 Y N N N N N -8.760 11.494 -24.187 -3.118 -1.581 -0.058 N1 HR3 16
HR3 N2 N2 N 0 1 N N N N N N -5.388 12.086 -24.114 0.182 -0.119 0.093 N2 HR3 17
HR3 O1 O1 O 0 1 N N N N N N 0.688 10.598 -23.969 6.452 0.097 0.298 O1 HR3 18
HR3 O2 O2 O 0 1 N N N N N N -11.260 11.830 -21.969 -5.900 -1.942 -0.157 O2 HR3 19
HR3 O3 O3 O 0 1 N N N N N N -11.360 11.207 -24.074 -6.114 0.267 -0.103 O3 HR3 20
HR3 O4 O4 O 0 1 N N N N N N -5.143 13.244 -21.579 -0.194 2.400 0.248 O4 HR3 21
HR3 O5 O5 O 0 1 N N N N N N -6.946 13.690 -20.408 -2.172 3.374 -0.005 O5 HR3 22
HR3 H11 H1 H 0 1 N N N N N N 2.494 9.825 -23.741 7.082 -0.456 -1.590 H11 HR3 23
HR3 H12 H2 H 0 1 N N N N N N 1.105 8.832 -23.183 6.622 1.253 -1.406 H12 HR3 24
HR3 H10 H3 H 0 1 N N N N N N 1.414 9.037 -24.941 8.157 0.666 -0.722 H10 HR3 25
HR3 H01 H4 H 0 1 N N N N N N -7.291 11.174 -25.409 -1.206 -2.367 -0.019 H01 HR3 26
HR3 H02 H5 H 0 1 N N N N N N -8.884 12.824 -21.263 -4.040 1.633 0.002 H02 HR3 27
HR3 H04 H6 H 0 1 N N N N N N -4.928 10.970 -25.831 0.818 -1.793 -0.998 H04 HR3 28
HR3 H05 H7 H 0 1 N N N N N N -5.230 10.006 -24.346 0.768 -2.016 0.768 H05 HR3 29
HR3 H06 H8 H 0 1 N N N N N N -2.971 12.806 -24.155 2.549 -1.165 2.178 H06 HR3 30
HR3 H07 H9 H 0 1 N N N N N N -0.630 12.502 -23.875 4.924 -0.534 2.330 H07 HR3 31
HR3 H08 H10 H 0 1 N N N N N N -0.916 8.451 -24.594 5.053 -0.034 -1.913 H08 HR3 32
HR3 H09 H11 H 0 1 N N N N N N -3.306 8.657 -24.928 2.673 -0.645 -2.053 H09 HR3 33
HR3 H03 H12 H 0 1 N N N N N N -4.831 12.304 -23.313 0.599 0.748 0.214 H03 HR3 34
HR3 H1 H13 H 0 1 N N N N N N -12.163 11.563 -22.098 -6.864 -2.013 -0.190 H1 HR3 35
HR3 H2 H14 H 0 1 N N N N N N -6.284 14.074 -19.845 -1.731 4.233 0.038 H2 HR3 36
#
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
HR3 C6 C7 SING N N 1
HR3 C6 N2 SING N N 2
HR3 C12 C7 DOUB Y N 3
HR3 C12 C11 SING Y N 4
HR3 C7 C8 SING Y N 5
HR3 C11 C10 DOUB Y N 6
HR3 C2 N1 DOUB Y N 7
HR3 C2 C1 SING Y N 8
HR3 C8 C9 DOUB Y N 9
HR3 C10 C9 SING Y N 10
HR3 C10 O1 SING N N 11
HR3 N1 C3 SING Y N 12
HR3 N2 C1 SING N N 13
HR3 O3 C14 DOUB N N 14
HR3 O1 C13 SING N N 15
HR3 C1 C5 DOUB Y N 16
HR3 C3 C14 SING N N 17
HR3 C3 C4 DOUB Y N 18
HR3 C14 O2 SING N N 19
HR3 C5 C4 SING Y N 20
HR3 C5 C15 SING N N 21
HR3 O4 C15 DOUB N N 22
HR3 C15 O5 SING N N 23
HR3 C13 H11 SING N N 24
HR3 C13 H12 SING N N 25
HR3 C13 H10 SING N N 26
HR3 C2 H01 SING N N 27
HR3 C4 H02 SING N N 28
HR3 C6 H04 SING N N 29
HR3 C6 H05 SING N N 30
HR3 C8 H06 SING N N 31
HR3 C9 H07 SING N N 32
HR3 C11 H08 SING N N 33
HR3 C12 H09 SING N N 34
HR3 N2 H03 SING N N 35
HR3 O2 H1 SING N N 36
HR3 O5 H2 SING N N 37
#
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
HR3 InChI InChI 1.03 InChI=1S/C15H14N2O5/c1-22-10-4-2-9(3-5-10)7-16-13-8-17-12(15(20)21)6-11(13)14(18)19/h2-6,8,16H,7H2,1H3,(H,18,19)(H,20,21)
HR3 InChIKey InChI 1.03 FRXQENHLNWKEGR-UHFFFAOYSA-N
HR3 SMILES_CANONICAL CACTVS 3.385 COc1ccc(CNc2cnc(cc2C(O)=O)C(O)=O)cc1
HR3 SMILES CACTVS 3.385 COc1ccc(CNc2cnc(cc2C(O)=O)C(O)=O)cc1
HR3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 COc1ccc(cc1)CNc2cnc(cc2C(=O)O)C(=O)O
HR3 SMILES "OpenEye OEToolkits" 2.0.7 COc1ccc(cc1)CNc2cnc(cc2C(=O)O)C(=O)O
#
_pdbx_chem_comp_identifier.comp_id HR3
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier "5-[(4-methoxyphenyl)methylamino]pyridine-2,4-dicarboxylic 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
HR3 'Create component' 2021-01-29 PDBJ
HR3 'Initial release' 2022-02-02 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 '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
HR3 C10 C 5.598 2.393 1
HR3 C13 C 3.000 2.393 2
HR3 C15 C 13.392 2.393 3
HR3 C1 C 12.093 0.142 4
HR3 C2 C 12.093 -1.357 5
HR3 C3 C 14.691 -1.357 6
HR3 C4 C 14.691 0.142 7
HR3 C5 C 13.392 0.892 8
HR3 C6 C 9.495 0.142 9
HR3 C7 C 8.196 0.892 10
HR3 C8 C 6.897 0.142 11
HR3 C9 C 5.598 0.892 12
HR3 C11 C 6.897 3.143 13
HR3 C12 C 8.196 2.393 14
HR3 C14 C 15.990 -2.107 15
HR3 N1 N 13.392 -2.107 16
HR3 N2 N 10.794 0.892 17
HR3 O1 O 4.299 3.143 18
HR3 O2 O 17.290 -1.357 19
HR3 O3 O 15.990 -3.607 20
HR3 O4 O 14.691 3.143 21
HR3 O5 O 12.093 3.143 22
#
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
HR3 C6 C7 SINGLE NONE 1
HR3 C6 N2 SINGLE NONE 2
HR3 C12 C7 DOUBLE NONE 3
HR3 C12 C11 SINGLE NONE 4
HR3 C7 C8 SINGLE NONE 5
HR3 C11 C10 DOUBLE NONE 6
HR3 C2 N1 DOUBLE NONE 7
HR3 C2 C1 SINGLE NONE 8
HR3 C8 C9 DOUBLE NONE 9
HR3 C10 C9 SINGLE NONE 10
HR3 C10 O1 SINGLE NONE 11
HR3 N1 C3 SINGLE NONE 12
HR3 N2 C1 SINGLE NONE 13
HR3 O3 C14 DOUBLE NONE 14
HR3 O1 C13 SINGLE NONE 15
HR3 C1 C5 DOUBLE NONE 16
HR3 C3 C14 SINGLE NONE 17
HR3 C3 C4 DOUBLE NONE 18
HR3 C14 O2 SINGLE NONE 19
HR3 C5 C4 SINGLE NONE 20
HR3 C5 C15 SINGLE NONE 21
HR3 O4 C15 DOUBLE NONE 22
HR3 C15 O5 SINGLE NONE 23
#
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
HR3 MurckoScaffold S1 scaffold c1ccc(CNc2cccnc2)cc1 InChI=1S/C12H12N2/c1-2-5-11(6-3-1)9-14-12-7-4-8-13-10-12/h1-8,10,14H,9H2 SQMRJGGCCLWSQR-UHFFFAOYSA-N
HR3 phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
HR3 pyridine F2 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-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
HR3 C10 S1 1
HR3 C1 S1 1
HR3 C2 S1 1
HR3 C3 S1 1
HR3 C4 S1 1
HR3 C5 S1 1
HR3 C6 S1 1
HR3 C7 S1 1
HR3 C8 S1 1
HR3 C9 S1 1
HR3 C11 S1 1
HR3 C12 S1 1
HR3 N1 S1 1
HR3 N2 S1 1
HR3 C10 F1 1
HR3 C11 F1 1
HR3 C12 F1 1
HR3 C7 F1 1
HR3 C8 F1 1
HR3 C9 F1 1
HR3 C2 F2 1
HR3 C1 F2 1
HR3 C5 F2 1
HR3 C4 F2 1
HR3 C3 F2 1
HR3 N1 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id HR3
_pdbe_chem_comp_rdkit_properties.exactmw 302.090
_pdbe_chem_comp_rdkit_properties.amw 302.286
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 22
_pdbe_chem_comp_rdkit_properties.NumAtoms 36
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.133
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_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 145.644
_pdbe_chem_comp_rdkit_properties.tpsa 108.750
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.092
_pdbe_chem_comp_rdkit_properties.CrippenMR 76.244
_pdbe_chem_comp_rdkit_properties.chi0v 10.436
_pdbe_chem_comp_rdkit_properties.chi1v 5.369
_pdbe_chem_comp_rdkit_properties.chi2v 2.135
_pdbe_chem_comp_rdkit_properties.chi3v 2.135
_pdbe_chem_comp_rdkit_properties.chi4v 1.215
_pdbe_chem_comp_rdkit_properties.chi0n 24.436
_pdbe_chem_comp_rdkit_properties.chi1n 12.133
_pdbe_chem_comp_rdkit_properties.chi2n 2.135
_pdbe_chem_comp_rdkit_properties.chi3n 2.135
_pdbe_chem_comp_rdkit_properties.chi4n 1.215
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -3.090
_pdbe_chem_comp_rdkit_properties.kappa1 5.275
_pdbe_chem_comp_rdkit_properties.kappa2 6.575
_pdbe_chem_comp_rdkit_properties.kappa3 3.512
_pdbe_chem_comp_rdkit_properties.Phi 1.576
#
_pdbe_chem_comp_external_mappings.comp_id HR3
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id HR3
#
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
HR3 C10 -4.353 -0.454 -0.394 ETKDGv3 1
HR3 C13 -6.581 -1.093 0.525 ETKDGv3 2
HR3 C15 2.240 -1.962 -0.299 ETKDGv3 3
HR3 C1 1.949 0.510 -0.097 ETKDGv3 4
HR3 C2 2.557 1.864 -0.160 ETKDGv3 5
HR3 C3 4.714 0.881 -0.507 ETKDGv3 6
HR3 C4 4.208 -0.362 -0.465 ETKDGv3 7
HR3 C5 2.752 -0.571 -0.264 ETKDGv3 8
HR3 C6 -0.434 1.394 -0.140 ETKDGv3 9
HR3 C7 -1.804 0.783 -0.243 ETKDGv3 10
HR3 C8 -2.723 0.823 0.920 ETKDGv3 11
HR3 C9 -3.927 0.243 0.850 ETKDGv3 12
HR3 C11 -3.513 -0.498 -1.438 ETKDGv3 13
HR3 C12 -2.182 0.137 -1.359 ETKDGv3 14
HR3 C14 6.154 1.117 -0.715 ETKDGv3 15
HR3 N1 3.835 2.006 -0.348 ETKDGv3 16
HR3 N2 0.550 0.370 0.207 ETKDGv3 17
HR3 O1 -5.606 -1.071 -0.511 ETKDGv3 18
HR3 O2 7.035 0.050 -0.872 ETKDGv3 19
HR3 O3 6.595 2.297 -0.751 ETKDGv3 20
HR3 O4 1.058 -2.209 -0.660 ETKDGv3 21
HR3 O5 3.088 -3.018 0.021 ETKDGv3 22
HR3 H11 -7.476 -1.642 0.169 ETKDGv3 23
HR3 H12 -6.880 -0.056 0.789 ETKDGv3 24
HR3 H10 -6.176 -1.612 1.419 ETKDGv3 25
HR3 H01 1.946 2.746 -0.031 ETKDGv3 26
HR3 H02 4.856 -1.221 -0.593 ETKDGv3 27
HR3 H04 -0.426 2.189 0.636 ETKDGv3 28
HR3 H05 -0.166 1.864 -1.112 ETKDGv3 29
HR3 H06 -2.421 1.322 1.832 ETKDGv3 30
HR3 H07 -4.581 0.287 1.711 ETKDGv3 31
HR3 H08 -3.805 -1.005 -2.349 ETKDGv3 32
HR3 H09 -1.516 0.071 -2.211 ETKDGv3 33
HR3 H03 0.246 -0.415 0.827 ETKDGv3 34
HR3 H1 8.025 0.210 -1.015 ETKDGv3 35
HR3 H2 2.762 -3.977 -0.014 ETKDGv3 36
#