data_3IP
#
_chem_comp.id 3IP
_chem_comp.name 3-(BENZYLOXY)PYRIDIN-2-AMINE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H12 N2 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2004-09-02
_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 200.236
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 3IP
_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 ?
_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
3IP N1 N1 N 0 1 N N N N N N 20.748 34.395 31.484 2.326 0.009 2.285 N1 3IP 1
3IP C2 C2 C 0 1 Y N N N N N 21.600 33.876 30.497 0.968 0.003 2.592 C2 3IP 2
3IP N3 N3 N 0 1 Y N N N N N 22.661 34.609 30.090 0.581 0.001 3.858 N3 3IP 3
3IP C4 C4 C 0 1 Y N N N N N 23.519 34.175 29.143 -0.695 -0.003 4.192 C4 3IP 4
3IP C5 C5 C 0 1 Y N N N N N 23.348 32.921 28.526 -1.682 -0.008 3.227 C5 3IP 5
3IP C6 C6 C 0 1 Y N N N N N 22.248 32.107 28.915 -1.322 -0.006 1.886 C6 3IP 6
3IP C7 C7 C 0 1 Y N N N N N 21.353 32.595 29.923 0.026 0.005 1.563 C7 3IP 7
3IP O8 O8 O 0 1 N N N N N N 20.254 31.892 30.372 0.424 0.007 0.263 O8 3IP 8
3IP C9 C9 C 0 1 N N N N N N 19.544 30.985 29.481 -0.762 -0.004 -0.532 C9 3IP 9
3IP C10 C10 C 0 1 Y N N N N N 18.114 30.821 29.993 -0.388 -0.002 -1.992 C10 3IP 10
3IP C11 C11 C 0 1 Y N N N N N 17.800 29.847 30.990 -0.206 -1.198 -2.660 C11 3IP 11
3IP C12 C12 C 0 1 Y N N N N N 16.458 29.698 31.478 0.136 -1.197 -3.999 C12 3IP 12
3IP C13 C13 C 0 1 Y N N N N N 15.417 30.530 30.968 0.296 0.000 -4.670 C13 3IP 13
3IP C14 C14 C 0 1 Y N N N N N 15.735 31.491 29.982 0.113 1.196 -4.002 C14 3IP 14
3IP C15 C15 C 0 1 Y N N N N N 17.057 31.641 29.499 -0.233 1.195 -2.664 C15 3IP 15
3IP H1N1 1H1N H 0 0 N N N N N N 19.948 33.842 31.791 2.984 0.012 2.998 H1N1 3IP 16
3IP H1N2 2H1N H 0 0 N N N N N N 20.925 35.312 31.895 2.614 0.006 1.359 H1N2 3IP 17
3IP H4 H4 H 0 1 N N N N N N 24.368 34.813 28.847 -0.972 -0.005 5.236 H4 3IP 18
3IP H5 H5 H 0 1 N N N N N N 24.055 32.575 27.754 -2.723 -0.013 3.513 H5 3IP 19
3IP H6 H6 H 0 1 N N N N N N 22.087 31.120 28.450 -2.076 -0.010 1.112 H6 3IP 20
3IP H9C1 1H9C H 0 0 N N N N N N 20.069 30.009 29.358 -1.342 -0.899 -0.307 H9C1 3IP 21
3IP H9C2 2H9C H 0 0 N N N N N N 19.582 31.315 28.417 -1.358 0.880 -0.309 H9C2 3IP 22
3IP H11 H11 H 0 1 N N N N N N 18.599 29.201 31.390 -0.331 -2.134 -2.136 H11 3IP 23
3IP H12 H12 H 0 1 N N N N N N 16.232 28.940 32.247 0.280 -2.132 -4.521 H12 3IP 24
3IP H13 H13 H 0 1 N N N N N N 14.383 30.425 31.337 0.565 0.001 -5.716 H13 3IP 25
3IP H14 H14 H 0 1 N N N N N N 14.937 32.138 29.580 0.238 2.132 -4.527 H14 3IP 26
3IP H15 H15 H 0 1 N N N N N N 17.272 32.402 28.730 -0.376 2.129 -2.143 H15 3IP 27
#
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
3IP N1 C2 SING N N 1
3IP N1 H1N1 SING N N 2
3IP N1 H1N2 SING N N 3
3IP C2 N3 DOUB Y N 4
3IP C2 C7 SING Y N 5
3IP N3 C4 SING Y N 6
3IP C4 C5 DOUB Y N 7
3IP C4 H4 SING N N 8
3IP C5 C6 SING Y N 9
3IP C5 H5 SING N N 10
3IP C6 C7 DOUB Y N 11
3IP C6 H6 SING N N 12
3IP C7 O8 SING N N 13
3IP O8 C9 SING N N 14
3IP C9 C10 SING N N 15
3IP C9 H9C1 SING N N 16
3IP C9 H9C2 SING N N 17
3IP C10 C11 DOUB Y N 18
3IP C10 C15 SING Y N 19
3IP C11 C12 SING Y N 20
3IP C11 H11 SING N N 21
3IP C12 C13 DOUB Y N 22
3IP C12 H12 SING N N 23
3IP C13 C14 SING Y N 24
3IP C13 H13 SING N N 25
3IP C14 C15 DOUB Y N 26
3IP C14 H14 SING N N 27
3IP C15 H15 SING N N 28
#
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
3IP SMILES ACDLabs 10.04 O(c1cccnc1N)Cc2ccccc2
3IP SMILES_CANONICAL CACTVS 3.341 Nc1ncccc1OCc2ccccc2
3IP SMILES CACTVS 3.341 Nc1ncccc1OCc2ccccc2
3IP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1ccc(cc1)COc2cccnc2N
3IP SMILES "OpenEye OEToolkits" 1.5.0 c1ccc(cc1)COc2cccnc2N
3IP InChI InChI 1.03 InChI=1S/C12H12N2O/c13-12-11(7-4-8-14-12)15-9-10-5-2-1-3-6-10/h1-8H,9H2,(H2,13,14)
3IP InChIKey InChI 1.03 NMCBWICNRJLKKM-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
3IP "SYSTEMATIC NAME" ACDLabs 10.04 3-(benzyloxy)pyridin-2-amine
3IP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 3-phenylmethoxypyridin-2-amine
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
3IP 'Create component' 2004-09-02 EBI
3IP 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id 3IP
_pdbe_chem_comp_drugbank_details.drugbank_id DB02352
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 3-(Benzyloxy)Pyridin-2-Amine
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_drugbank_classification.comp_id 3IP
_pdbe_chem_comp_drugbank_classification.drugbank_id DB02352
_pdbe_chem_comp_drugbank_classification.parent 'Aminopyridines and derivatives'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Pyridines and derivatives'
_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 aminopyridines and derivatives. These are organic heterocyclic compounds containing an amino group attached to a pyridine 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
3IP DB02352 'Leukotriene A-4 hydrolase' Humans P09960 unknown 1
3IP DB02352 'Mitogen-activated protein kinase 14' Humans Q16539 unknown 2
#
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
3IP N1 N 10.794 -1.875 1
3IP C2 C 10.794 -0.375 2
3IP N3 N 12.093 0.375 3
3IP C4 C 12.093 1.875 4
3IP C5 C 10.794 2.625 5
3IP C6 C 9.495 1.875 6
3IP C7 C 9.495 0.375 7
3IP O8 O 8.196 -0.375 8
3IP C9 C 6.897 0.375 9
3IP C10 C 5.598 -0.375 10
3IP C11 C 4.299 0.375 11
3IP C12 C 3.000 -0.375 12
3IP C13 C 3.000 -1.875 13
3IP C14 C 4.299 -2.625 14
3IP C15 C 5.598 -1.875 15
#
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
3IP N1 C2 SINGLE NONE 1
3IP C2 N3 DOUBLE NONE 2
3IP C2 C7 SINGLE NONE 3
3IP N3 C4 SINGLE NONE 4
3IP C4 C5 DOUBLE NONE 5
3IP C5 C6 SINGLE NONE 6
3IP C6 C7 DOUBLE NONE 7
3IP C7 O8 SINGLE NONE 8
3IP O8 C9 SINGLE NONE 9
3IP C9 C10 SINGLE NONE 10
3IP C10 C11 DOUBLE NONE 11
3IP C10 C15 SINGLE NONE 12
3IP C11 C12 SINGLE NONE 13
3IP C12 C13 DOUBLE NONE 14
3IP C13 C14 SINGLE NONE 15
3IP C14 C15 DOUBLE 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
3IP MurckoScaffold S1 scaffold c1ccc(COc2cccnc2)cc1 InChI=1S/C12H11NO/c1-2-5-11(6-3-1)10-14-12-7-4-8-13-9-12/h1-9H,10H2 LLWFWIZOFFLRKC-UHFFFAOYSA-N
3IP phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
3IP 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
3IP C2 S1 1
3IP N3 S1 1
3IP C4 S1 1
3IP C5 S1 1
3IP C6 S1 1
3IP C7 S1 1
3IP O8 S1 1
3IP C9 S1 1
3IP C10 S1 1
3IP C11 S1 1
3IP C12 S1 1
3IP C13 S1 1
3IP C14 S1 1
3IP C15 S1 1
3IP C10 F1 1
3IP C11 F1 1
3IP C12 F1 1
3IP C13 F1 1
3IP C14 F1 1
3IP C15 F1 1
3IP C2 F2 1
3IP C7 F2 1
3IP C6 F2 1
3IP C5 F2 1
3IP C4 F2 1
3IP N3 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 3IP
_pdbe_chem_comp_rdkit_properties.exactmw 200.095
_pdbe_chem_comp_rdkit_properties.amw 200.241
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 27
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.083
_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 105.502
_pdbe_chem_comp_rdkit_properties.tpsa 48.140
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.345
_pdbe_chem_comp_rdkit_properties.CrippenMR 57.723
_pdbe_chem_comp_rdkit_properties.chi0v 7.303
_pdbe_chem_comp_rdkit_properties.chi1v 3.829
_pdbe_chem_comp_rdkit_properties.chi2v 1.352
_pdbe_chem_comp_rdkit_properties.chi3v 1.352
_pdbe_chem_comp_rdkit_properties.chi4v 0.747
_pdbe_chem_comp_rdkit_properties.chi0n 19.303
_pdbe_chem_comp_rdkit_properties.chi1n 9.723
_pdbe_chem_comp_rdkit_properties.chi2n 1.352
_pdbe_chem_comp_rdkit_properties.chi3n 1.352
_pdbe_chem_comp_rdkit_properties.chi4n 0.747
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.030
_pdbe_chem_comp_rdkit_properties.kappa1 2.755
_pdbe_chem_comp_rdkit_properties.kappa2 4.461
_pdbe_chem_comp_rdkit_properties.kappa3 2.465
_pdbe_chem_comp_rdkit_properties.Phi 0.819
#
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
3IP UniChem ChEMBL CHEMBL194009
3IP UniChem DrugBank DB02352
3IP UniChem PDBe 3IP
3IP UniChem ZINC ZINC000018996118
3IP UniChem eMolecules 481893
3IP UniChem fdasrs IYW7T7718Z
3IP UniChem SureChEMBL SCHEMBL105010
3IP UniChem 'PubChem TPHARMA' 14794272
3IP UniChem BindingDb 13337
3IP UniChem 'EPA CompTox Dashboard' DTXSID50178748
3IP UniChem BRENDA 159014
3IP UniChem ChemicalBook CB3703762
3IP UniChem 'Probes And Drugs' PD008020
3IP UniChem Nikkaji J236.497B
3IP UniChem PubChem 90334
3IP UniChem Mcule MCULE-1376535850
3IP UniChem ACTor 24016-03-3
#
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
3IP N1 2.906 -2.014 1.073 ETKDGv3 1
3IP C2 2.683 -0.643 0.740 ETKDGv3 2
3IP N3 3.433 0.278 1.278 ETKDGv3 3
3IP C4 3.254 1.672 0.984 ETKDGv3 4
3IP C5 2.297 2.060 0.137 ETKDGv3 5
3IP C6 1.431 1.045 -0.491 ETKDGv3 6
3IP C7 1.604 -0.261 -0.207 ETKDGv3 7
3IP O8 0.810 -1.274 -0.773 ETKDGv3 8
3IP C9 -0.329 -1.069 -1.611 ETKDGv3 9
3IP C10 -1.474 -0.493 -0.821 ETKDGv3 10
3IP C11 -2.155 0.578 -1.270 ETKDGv3 11
3IP C12 -3.285 1.122 -0.488 ETKDGv3 12
3IP C13 -3.643 0.545 0.665 ETKDGv3 13
3IP C14 -2.912 -0.641 1.156 ETKDGv3 14
3IP C15 -1.886 -1.136 0.452 ETKDGv3 15
3IP H1N1 3.665 -2.278 1.740 ETKDGv3 16
3IP H1N2 2.319 -2.773 0.661 ETKDGv3 17
3IP H4 3.897 2.406 1.452 ETKDGv3 18
3IP H5 2.157 3.109 -0.090 ETKDGv3 19
3IP H6 0.668 1.380 -1.179 ETKDGv3 20
3IP H9C1 -0.648 -2.052 -2.015 ETKDGv3 21
3IP H9C2 -0.050 -0.433 -2.479 ETKDGv3 22
3IP H11 -1.885 1.057 -2.203 ETKDGv3 23
3IP H12 -3.821 1.989 -0.850 ETKDGv3 24
3IP H13 -4.471 0.943 1.238 ETKDGv3 25
3IP H14 -3.208 -1.109 2.086 ETKDGv3 26
3IP H15 -1.356 -2.007 0.816 ETKDGv3 27
#