data_PHN
#
_chem_comp.id PHN
_chem_comp.name 1,10-PHENANTHROLINE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H8 N2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2011-06-04
_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 180.205
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PHN
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 2LIG
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
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
PHN N1 N1 N 0 1 Y N N N N N -2.050 49.911 45.401 -1.511 0.000 -1.424 N1 PHN 1
PHN C2 C2 C 0 1 Y N N N N N -3.215 49.842 44.670 -1.513 -0.000 -2.738 C2 PHN 2
PHN C3 C3 C 0 1 Y N N N N N -4.300 50.747 44.944 -0.329 -0.000 -3.466 C3 PHN 3
PHN C4 C4 C 0 1 Y N N N N N -4.140 51.721 45.858 0.872 0.000 -2.813 C4 PHN 4
PHN C4A C4A C 0 1 Y N N N N N -2.974 51.791 46.588 0.866 0.000 -1.408 C4A PHN 5
PHN C5 C5 C 0 1 Y N N N N N -2.773 52.835 47.411 2.073 0.000 -0.674 C5 PHN 6
PHN C6 C6 C 0 1 Y N N N N N -1.487 52.974 47.959 2.073 0.000 0.674 C6 PHN 7
PHN C6A C6A C 0 1 Y N N N N N -0.522 52.139 47.776 0.866 0.000 1.408 C6A PHN 8
PHN C7 C7 C 0 1 Y N N N N N 0.643 52.208 48.415 0.872 -0.000 2.813 C7 PHN 9
PHN C8 C8 C 0 1 Y N N N N N 1.527 51.234 48.324 -0.329 -0.000 3.466 C8 PHN 10
PHN C9 C9 C 0 1 Y N N N N N 1.366 50.120 47.502 -1.513 -0.000 2.738 C9 PHN 11
PHN N10 N10 N 0 1 Y N N N N N 0.201 50.050 46.771 -1.511 0.000 1.424 N10 PHN 12
PHN C10 C10 C 0 1 Y N N N N N -0.723 51.095 46.863 -0.374 0.000 0.734 C10 PHN 13
PHN C1A C1A C 0 1 Y N N N N N -1.969 50.886 46.314 -0.374 0.000 -0.734 C1A PHN 14
PHN H2 H2 H 0 1 N N N N N N -3.277 49.075 43.879 -2.456 -0.000 -3.264 H2 PHN 15
PHN H3 H3 H 0 1 N N N N N N -5.279 50.692 44.440 -0.358 -0.004 -4.546 H3 PHN 16
PHN H4 H4 H 0 1 N N N N N N -4.952 52.451 46.006 1.802 -0.000 -3.363 H4 PHN 17
PHN H5 H5 H 0 1 N N N N N N -3.604 53.528 47.621 3.015 -0.000 -1.203 H5 PHN 18
PHN H6 H6 H 0 1 N N N N N N -1.205 53.827 48.599 3.015 -0.000 1.203 H6 PHN 19
PHN H7 H7 H 0 1 N N N N N N 0.880 53.090 49.032 1.802 -0.000 3.363 H7 PHN 20
PHN H8 H8 H 0 1 N N N N N N 2.425 51.354 48.952 -0.358 -0.001 4.546 H8 PHN 21
PHN H9 H9 H 0 1 N N N N N N 2.129 49.326 47.432 -2.456 -0.000 3.264 H9 PHN 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
PHN N1 C2 DOUB Y N 1
PHN N1 C1A SING Y N 2
PHN C2 C3 SING Y N 3
PHN C2 H2 SING N N 4
PHN C3 C4 DOUB Y N 5
PHN C3 H3 SING N N 6
PHN C4 C4A SING Y N 7
PHN C4 H4 SING N N 8
PHN C4A C5 DOUB Y N 9
PHN C4A C1A SING Y N 10
PHN C5 C6 SING Y N 11
PHN C5 H5 SING N N 12
PHN C6 C6A DOUB Y N 13
PHN C6 H6 SING N N 14
PHN C6A C7 SING Y N 15
PHN C6A C10 SING Y N 16
PHN C7 C8 DOUB Y N 17
PHN C7 H7 SING N N 18
PHN C8 C9 SING Y N 19
PHN C8 H8 SING N N 20
PHN C9 N10 DOUB Y N 21
PHN C9 H9 SING N N 22
PHN N10 C10 SING Y N 23
PHN C10 C1A DOUB Y N 24
#
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
PHN SMILES ACDLabs 10.04 n1c3c(ccc1)ccc2cccnc23
PHN SMILES_CANONICAL CACTVS 3.341 c1cnc2c(c1)ccc3cccnc23
PHN SMILES CACTVS 3.341 c1cnc2c(c1)ccc3cccnc23
PHN SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1cc2ccc3cccnc3c2nc1
PHN SMILES "OpenEye OEToolkits" 1.5.0 c1cc2ccc3cccnc3c2nc1
PHN InChI InChI 1.03 InChI=1S/C12H8N2/c1-3-9-5-6-10-4-2-8-14-12(10)11(9)13-7-1/h1-8H
PHN InChIKey InChI 1.03 DGEZNRSVGBDHLK-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
PHN "SYSTEMATIC NAME" ACDLabs 10.04 1,10-phenanthroline
PHN "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 1,10-phenanthroline
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
PHN 'Create component' 1999-07-08 RCSB
PHN 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id PHN
_pdbe_chem_comp_drugbank_details.drugbank_id DB02365
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 1,10-Phenanthroline
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 66-71-7
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
PHN 1,10-Phenanthroline DrugBank ?
PHN O-Phenanthroline DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id PHN
_pdbe_chem_comp_drugbank_classification.drugbank_id DB02365
_pdbe_chem_comp_drugbank_classification.parent Phenanthrolines
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class Phenanthrolines
_pdbe_chem_comp_drugbank_classification.superclass 'Organoheterocyclic compounds'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as phenanthrolines. These are aromatic polycyclic compounds containing the phenanthroline skeleton, which is a derivative of phenanthrene, and consists of two pyridine rings non-linearly joined by a benzene ring.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
PHN DB02365 'Metallo-beta-lactamase L1 type 3' 'Pseudomonas maltophilia' P52700 unknown 1
PHN DB02365 'Methyl-accepting chemotaxis protein II' 'Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)' P02941 unknown 2
#
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
PHN N1 N 6.975 1.911 1
PHN C2 C 8.322 2.703 2
PHN C3 C 9.675 1.922 3
PHN C4 C 9.663 0.359 4
PHN C4A C 8.298 -0.401 5
PHN C5 C 8.298 -1.901 6
PHN C6 C 6.999 -2.651 7
PHN C6A C 5.700 -1.901 8
PHN C7 C 4.359 -2.703 9
PHN C8 C 3.000 -1.932 10
PHN C9 C 3.000 -0.370 11
PHN N10 N 4.359 0.401 12
PHN C10 C 5.700 -0.401 13
PHN C1A C 6.999 0.349 14
#
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
PHN N1 C2 DOUBLE NONE 1
PHN N1 C1A SINGLE NONE 2
PHN C2 C3 SINGLE NONE 3
PHN C3 C4 DOUBLE NONE 4
PHN C4 C4A SINGLE NONE 5
PHN C4A C5 SINGLE NONE 6
PHN C4A C1A DOUBLE NONE 7
PHN C5 C6 DOUBLE NONE 8
PHN C6 C6A SINGLE NONE 9
PHN C6A C7 SINGLE NONE 10
PHN C6A C10 DOUBLE NONE 11
PHN C7 C8 DOUBLE NONE 12
PHN C8 C9 SINGLE NONE 13
PHN C9 N10 DOUBLE NONE 14
PHN N10 C10 SINGLE NONE 15
PHN C10 C1A SINGLE NONE 16
#
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
PHN MurckoScaffold S1 scaffold c1cnc2c(c1)ccc1cccnc12 InChI=1S/C12H8N2/c1-3-9-5-6-10-4-2-8-14-12(10)11(9)13-7-1/h1-8H DGEZNRSVGBDHLK-UHFFFAOYSA-N
PHN phenanthroline F1 fragment c1cnc2c(c1)ccc1cccnc12 InChI=1S/C12H8N2/c1-3-9-5-6-10-4-2-8-14-12(10)11(9)13-7-1/h1-8H DGEZNRSVGBDHLK-UHFFFAOYSA-N
PHN phenyl F2 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
PHN pyridine F3 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N
PHN quinoline F4 fragment c1ccc2ncccc2c1 InChI=1S/C9H7N/c1-2-6-9-8(4-1)5-3-7-10-9/h1-7H SMWDFEZZVXVKRB-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
PHN N1 S1 1
PHN C2 S1 1
PHN C3 S1 1
PHN C4 S1 1
PHN C4A S1 1
PHN C5 S1 1
PHN C6 S1 1
PHN C6A S1 1
PHN C7 S1 1
PHN C8 S1 1
PHN C9 S1 1
PHN N10 S1 1
PHN C10 S1 1
PHN C1A S1 1
PHN C3 F1 1
PHN C2 F1 1
PHN N1 F1 1
PHN C1A F1 1
PHN C4A F1 1
PHN C4 F1 1
PHN C5 F1 1
PHN C6 F1 1
PHN C6A F1 1
PHN C10 F1 1
PHN N10 F1 1
PHN C9 F1 1
PHN C8 F1 1
PHN C7 F1 1
PHN C4A F2 1
PHN C5 F2 1
PHN C6 F2 1
PHN C6A F2 1
PHN C10 F2 1
PHN C1A F2 1
PHN C2 F3 1
PHN C3 F3 1
PHN C4 F3 1
PHN C4A F3 1
PHN C1A F3 1
PHN N1 F3 1
PHN C9 F3 2
PHN C8 F3 2
PHN C7 F3 2
PHN C6A F3 2
PHN C10 F3 2
PHN N10 F3 2
PHN C5 F4 1
PHN C6 F4 1
PHN C6A F4 1
PHN C10 F4 1
PHN C1A F4 1
PHN C4A F4 1
PHN N10 F4 1
PHN C9 F4 1
PHN C8 F4 1
PHN C7 F4 1
PHN C6 F4 2
PHN C5 F4 2
PHN C4A F4 2
PHN C1A F4 2
PHN C10 F4 2
PHN C6A F4 2
PHN N1 F4 2
PHN C2 F4 2
PHN C3 F4 2
PHN C4 F4 2
#
_pdbe_chem_comp_rdkit_properties.comp_id PHN
_pdbe_chem_comp_rdkit_properties.exactmw 180.069
_pdbe_chem_comp_rdkit_properties.amw 180.210
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 0
_pdbe_chem_comp_rdkit_properties.NumHBD 0
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 22
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 3
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_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 92.474
_pdbe_chem_comp_rdkit_properties.tpsa 25.780
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.926
_pdbe_chem_comp_rdkit_properties.CrippenMR 52.632
_pdbe_chem_comp_rdkit_properties.chi0v 6.894
_pdbe_chem_comp_rdkit_properties.chi1v 3.894
_pdbe_chem_comp_rdkit_properties.chi2v 1.833
_pdbe_chem_comp_rdkit_properties.chi3v 1.833
_pdbe_chem_comp_rdkit_properties.chi4v 1.227
_pdbe_chem_comp_rdkit_properties.chi0n 14.894
_pdbe_chem_comp_rdkit_properties.chi1n 7.894
_pdbe_chem_comp_rdkit_properties.chi2n 1.833
_pdbe_chem_comp_rdkit_properties.chi3n 1.833
_pdbe_chem_comp_rdkit_properties.chi4n 1.227
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.960
_pdbe_chem_comp_rdkit_properties.kappa1 3.021
_pdbe_chem_comp_rdkit_properties.kappa2 2.771
_pdbe_chem_comp_rdkit_properties.kappa3 0.973
_pdbe_chem_comp_rdkit_properties.Phi 0.598
#
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
PHN UniChem DrugBank DB02365
PHN UniChem 'KEGG LIGAND' C00604
PHN UniChem ChEBI 44975
PHN UniChem ZINC ZINC000000164363
PHN UniChem eMolecules 480572
PHN UniChem fdasrs W4X6ZO7939
PHN UniChem HMDB HMDB0244053
PHN UniChem NMRShiftDB 20127648
PHN UniChem LINCS LSM-18864
PHN UniChem ACTor 66-71-7
PHN UniChem 'EPA CompTox Dashboard' DTXSID1025857
PHN UniChem BRENDA 118217
PHN UniChem BRENDA 15433
PHN UniChem BRENDA 239
PHN UniChem BRENDA 25947
PHN UniChem BRENDA 62
PHN UniChem BRENDA 6650
PHN UniChem BRENDA 66663
PHN UniChem BRENDA 69251
PHN UniChem BRENDA 94537
PHN UniChem ChemicalBook CB4283203
PHN UniChem rxnorm O-PHENANTHROLINE
PHN UniChem MedChemExpress HY-W004544
PHN UniChem 'Probes And Drugs' PD002621
PHN UniChem CCDC OPENAN
PHN UniChem BindingDb 50092158
PHN UniChem SureChEMBL SCHEMBL8312
PHN UniChem 'PubChem TPHARMA' 14772738
PHN UniChem PubChem 1318
PHN UniChem Mcule MCULE-2911225521
PHN UniChem Nikkaji J4.844E
#
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
PHN N1 1.551 -1.664 0.017 ETKDGv3 1
PHN C2 2.852 -1.630 0.008 ETKDGv3 2
PHN C3 3.561 -0.335 -0.017 ETKDGv3 3
PHN C4 2.854 0.800 -0.030 ETKDGv3 4
PHN C4A 1.377 0.745 -0.020 ETKDGv3 5
PHN C5 0.571 1.988 -0.035 ETKDGv3 6
PHN C6 -0.766 1.921 -0.026 ETKDGv3 7
PHN C6A -1.444 0.605 -0.001 ETKDGv3 8
PHN C7 -2.920 0.514 0.010 ETKDGv3 9
PHN C8 -3.510 -0.686 0.032 ETKDGv3 10
PHN C9 -2.677 -1.905 0.047 ETKDGv3 11
PHN N10 -1.378 -1.809 0.037 ETKDGv3 12
PHN C10 -0.714 -0.532 0.013 ETKDGv3 13
PHN C1A 0.764 -0.459 0.003 ETKDGv3 14
PHN H2 3.415 -2.554 0.019 ETKDGv3 15
PHN H3 4.643 -0.307 -0.024 ETKDGv3 16
PHN H4 3.366 1.755 -0.048 ETKDGv3 17
PHN H5 1.062 2.953 -0.053 ETKDGv3 18
PHN H6 -1.350 2.833 -0.037 ETKDGv3 19
PHN H7 -3.523 1.413 -0.001 ETKDGv3 20
PHN H8 -4.589 -0.766 0.040 ETKDGv3 21
PHN H9 -3.145 -2.880 0.065 ETKDGv3 22
#