data_26D
#
_chem_comp.id 26D
_chem_comp.name PYRIDINE-2,6-DIAMINE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C5 H7 N3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2005-08-23
_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 109.129
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 26D
_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 2ANZ
_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
26D N1 N1 N 0 1 N N N N N N -18.674 -3.269 -3.774 2.346 -1.016 0.001 N1 26D 1
26D C3 C3 C 0 1 Y N N N N N -17.508 -3.199 -4.407 1.156 -0.298 0.001 C3 26D 2
26D N3 N3 N 0 1 Y N N N N N -17.375 -3.744 -5.628 0.000 -0.945 -0.004 N3 26D 3
26D C5 C5 C 0 1 Y N N N N N -16.424 -2.568 -3.804 1.191 1.091 0.000 C5 26D 4
26D C6 C6 C 0 1 Y N N N N N -15.214 -2.515 -4.488 0.000 1.799 0.000 C6 26D 5
26D C4 C4 C 0 1 Y N N N N N -15.102 -3.087 -5.750 -1.191 1.091 0.000 C4 26D 6
26D C2 C2 C 0 1 Y N N N N N -16.218 -3.708 -6.307 -1.156 -0.298 0.001 C2 26D 7
26D N2 N2 N 0 1 N N N N N N -16.133 -4.276 -7.505 -2.346 -1.016 0.001 N2 26D 8
26D HN11 1HN1 H 0 0 N N N N N N -19.229 -2.471 -4.009 3.195 -0.547 0.001 HN11 26D 9
26D HN12 2HN1 H 0 0 N N N N N N -18.517 -3.287 -2.787 2.327 -1.986 0.006 HN12 26D 10
26D H5 H5 H 0 1 N N N N N N -16.521 -2.127 -2.823 2.136 1.614 0.000 H5 26D 11
26D H6 H6 H 0 1 N N N N N N -14.361 -2.029 -4.038 0.000 2.879 0.000 H6 26D 12
26D H4 H4 H 0 1 N N N N N N -14.167 -3.051 -6.289 -2.136 1.614 0.000 H4 26D 13
26D HN21 1HN2 H 0 0 N N N N N N -15.297 -4.822 -7.556 -3.195 -0.547 0.001 HN21 26D 14
26D HN22 2HN2 H 0 0 N N N N N N -16.112 -3.567 -8.210 -2.327 -1.986 0.002 HN22 26D 15
#
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
26D N1 C3 SING N N 1
26D N1 HN11 SING N N 2
26D N1 HN12 SING N N 3
26D C3 N3 SING Y N 4
26D C3 C5 DOUB Y N 5
26D N3 C2 DOUB Y N 6
26D C5 C6 SING Y N 7
26D C5 H5 SING N N 8
26D C6 C4 DOUB Y N 9
26D C6 H6 SING N N 10
26D C4 C2 SING Y N 11
26D C4 H4 SING N N 12
26D C2 N2 SING N N 13
26D N2 HN21 SING N N 14
26D N2 HN22 SING N N 15
#
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
26D SMILES ACDLabs 10.04 n1c(N)cccc1N
26D SMILES_CANONICAL CACTVS 3.341 Nc1cccc(N)n1
26D SMILES CACTVS 3.341 Nc1cccc(N)n1
26D SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1cc(nc(c1)N)N
26D SMILES "OpenEye OEToolkits" 1.5.0 c1cc(nc(c1)N)N
26D InChI InChI 1.03 InChI=1S/C5H7N3/c6-4-2-1-3-5(7)8-4/h1-3H,(H4,6,7,8)
26D InChIKey InChI 1.03 VHNQIURBCCNWDN-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
26D "SYSTEMATIC NAME" ACDLabs 10.04 pyridine-2,6-diamine
26D "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 pyridine-2,6-diamine
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
26D 'Create component' 2005-08-23 RCSB
26D 'Modify descriptor' 2011-06-04 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
26D N1 N 3.805 -1.035 1
26D C3 C 5.104 -0.285 2
26D N3 N 6.404 -1.035 3
26D C5 C 5.104 1.215 4
26D C6 C 6.404 1.965 5
26D C4 C 7.702 1.215 6
26D C2 C 7.702 -0.285 7
26D N2 N 9.002 -1.035 8
#
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
26D N1 C3 SINGLE NONE 1
26D C3 N3 DOUBLE NONE 2
26D C3 C5 SINGLE NONE 3
26D N3 C2 SINGLE NONE 4
26D C5 C6 DOUBLE NONE 5
26D C6 C4 SINGLE NONE 6
26D C4 C2 DOUBLE NONE 7
26D C2 N2 SINGLE NONE 8
#
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
26D MurckoScaffold S1 scaffold c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N
26D pyridine F1 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
26D C3 S1 1
26D N3 S1 1
26D C5 S1 1
26D C6 S1 1
26D C4 S1 1
26D C2 S1 1
26D C3 F1 1
26D C5 F1 1
26D C6 F1 1
26D C4 F1 1
26D C2 F1 1
26D N3 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 26D
_pdbe_chem_comp_rdkit_properties.exactmw 109.064
_pdbe_chem_comp_rdkit_properties.amw 109.132
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 8
_pdbe_chem_comp_rdkit_properties.NumAtoms 15
_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 57.398
_pdbe_chem_comp_rdkit_properties.tpsa 64.930
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.515
_pdbe_chem_comp_rdkit_properties.CrippenMR 31.414
_pdbe_chem_comp_rdkit_properties.chi0v 3.842
_pdbe_chem_comp_rdkit_properties.chi1v 1.894
_pdbe_chem_comp_rdkit_properties.chi2v 0.560
_pdbe_chem_comp_rdkit_properties.chi3v 0.560
_pdbe_chem_comp_rdkit_properties.chi4v 0.299
_pdbe_chem_comp_rdkit_properties.chi0n 10.842
_pdbe_chem_comp_rdkit_properties.chi1n 5.183
_pdbe_chem_comp_rdkit_properties.chi2n 0.560
_pdbe_chem_comp_rdkit_properties.chi3n 0.560
_pdbe_chem_comp_rdkit_properties.chi4n 0.299
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.250
_pdbe_chem_comp_rdkit_properties.kappa1 1.180
_pdbe_chem_comp_rdkit_properties.kappa2 1.694
_pdbe_chem_comp_rdkit_properties.kappa3 0.872
_pdbe_chem_comp_rdkit_properties.Phi 0.250
#
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
26D UniChem ChEMBL CHEMBL339234
26D UniChem PDBe 26D
26D UniChem ZINC ZINC000000333587
26D UniChem eMolecules 498383
26D UniChem fdasrs K89AB8CKG6
26D UniChem PubChem 8861
26D UniChem NMRShiftDB 20028165
26D UniChem ACTor 141-86-6
26D UniChem Nikkaji J38.340F
26D UniChem 'EPA CompTox Dashboard' DTXSID0040127
26D UniChem ChemicalBook CB0236195
26D UniChem SureChEMBL SCHEMBL64599
26D UniChem 'PubChem TPHARMA' 15213228
26D UniChem Mcule MCULE-6883306972
#
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
26D N1 -2.318 -1.326 0.083 ETKDGv3 1
26D C3 -1.151 -0.510 0.002 ETKDGv3 2
26D N3 0.019 -1.019 0.271 ETKDGv3 3
26D C5 -1.260 0.914 -0.386 ETKDGv3 4
26D C6 -0.153 1.660 -0.455 ETKDGv3 5
26D C4 1.159 1.059 -0.146 ETKDGv3 6
26D C2 1.225 -0.236 0.203 ETKDGv3 7
26D N2 2.480 -0.845 0.508 ETKDGv3 8
26D HN11 -2.244 -2.331 0.356 ETKDGv3 9
26D HN12 -3.260 -0.930 -0.130 ETKDGv3 10
26D H5 -2.225 1.349 -0.612 ETKDGv3 11
26D H6 -0.216 2.703 -0.737 ETKDGv3 12
26D H4 2.054 1.666 -0.203 ETKDGv3 13
26D HN21 3.371 -0.300 0.467 ETKDGv3 14
26D HN22 2.520 -1.852 0.778 ETKDGv3 15
#