data_09P
#
_chem_comp.id 09P
_chem_comp.name 1-(5-ethoxypyridin-3-yl)-1,4-diazepane
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H19 N3 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2011-11-07
_chem_comp.pdbx_modified_date 2011-12-09
_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 221.299
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 09P
_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 3U8K
_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
09P C1 C1 C 0 1 N N N N N N 86.720 73.057 -11.163 2.914 1.785 0.668 C1 09P 1
09P N1 N1 N 0 1 N N N N N N 85.774 73.269 -12.282 4.044 1.275 -0.141 N1 09P 2
09P C2 C2 C 0 1 N N N N N N 85.584 72.171 -13.263 4.339 -0.086 0.229 C2 09P 3
09P C3 C3 C 0 1 N N N N N N 84.763 71.004 -12.676 3.625 -1.115 -0.674 C3 09P 4
09P C4 C4 C 0 1 N N N N N N 85.318 70.461 -11.350 2.175 -0.690 -0.988 C4 09P 5
09P N2 N2 N 0 1 N N N N N N 85.001 71.390 -10.252 1.499 -0.137 0.158 N2 09P 6
09P C5 C5 C 0 1 N N N N N N 86.080 72.357 -9.945 1.622 1.339 0.153 C5 09P 7
09P C6 C6 C 0 1 Y N N N N N 81.452 71.339 -8.165 -2.433 -1.373 0.250 C6 09P 8
09P C7 C7 C 0 1 Y N N N N N 81.531 70.530 -9.308 -2.173 -0.027 0.031 C7 09P 9
09P C8 C8 C 0 1 Y N N N N N 82.753 70.550 -10.028 -0.854 0.410 -0.004 C8 09P 10
09P C9 C9 C 0 1 Y N N N N N 83.826 71.357 -9.585 0.157 -0.527 0.184 C9 09P 11
09P C10 C10 C 0 1 Y N N N N N 83.606 72.118 -8.420 -0.185 -1.857 0.398 C10 09P 12
09P N3 N3 N 0 1 Y N N N N N 82.451 72.115 -7.729 -1.449 -2.232 0.424 N3 09P 13
09P O1 O1 O 0 1 N N N N N N 80.414 69.788 -9.663 -3.194 0.851 -0.148 O1 09P 14
09P C11 C11 C 0 1 N N N N N N 80.372 69.201 -10.961 -4.521 0.322 -0.099 C11 09P 15
09P C12 C12 C 0 1 N N N N N N 80.013 67.728 -10.807 -5.529 1.452 -0.320 C12 09P 16
09P H1 H1 H 0 1 N N N N N N 87.546 72.428 -11.526 3.027 1.434 1.694 H1 09P 17
09P H2 H2 H 0 1 N N N N N N 87.093 74.039 -10.838 2.940 2.875 0.663 H2 09P 18
09P H3 H3 H 0 1 N N N N N N 86.112 74.057 -12.797 4.858 1.863 -0.037 H3 09P 19
09P H5 H5 H 0 1 N N N N N N 86.573 71.790 -13.560 5.415 -0.245 0.162 H5 09P 20
09P H6 H6 H 0 1 N N N N N N 85.050 72.570 -14.138 4.025 -0.247 1.261 H6 09P 21
09P H7 H7 H 0 1 N N N N N N 83.740 71.364 -12.495 4.178 -1.211 -1.609 H7 09P 22
09P H8 H8 H 0 1 N N N N N N 84.765 70.183 -13.408 3.611 -2.081 -0.170 H8 09P 23
09P H9 H9 H 0 1 N N N N N N 84.863 69.482 -11.140 2.191 0.057 -1.782 H9 09P 24
09P H10 H10 H 0 1 N N N N N N 86.410 70.353 -11.430 1.621 -1.561 -1.338 H10 09P 25
09P H11 H11 H 0 1 N N N N N N 86.878 71.806 -9.425 0.830 1.762 0.771 H11 09P 26
09P H12 H12 H 0 1 N N N N N N 85.648 73.140 -9.304 1.504 1.700 -0.868 H12 09P 27
09P H13 H13 H 0 1 N N N N N N 80.530 71.335 -7.603 -3.455 -1.720 0.282 H13 09P 28
09P H14 H14 H 0 1 N N N N N N 82.864 69.947 -10.917 -0.620 1.451 -0.172 H14 09P 29
09P H15 H15 H 0 1 N N N N N N 84.412 72.741 -8.060 0.592 -2.592 0.545 H15 09P 30
09P H16 H16 H 0 1 N N N N N N 81.354 69.298 -11.447 -4.641 -0.430 -0.879 H16 09P 31
09P H17 H17 H 0 1 N N N N N N 79.615 69.708 -11.577 -4.694 -0.134 0.875 H17 09P 32
09P H18 H18 H 0 1 N N N N N N 79.975 67.254 -11.799 -5.355 1.908 -1.295 H18 09P 33
09P H19 H19 H 0 1 N N N N N N 80.774 67.228 -10.191 -6.541 1.048 -0.283 H19 09P 34
09P H20 H20 H 0 1 N N N N N N 79.031 67.639 -10.320 -5.409 2.204 0.460 H20 09P 35
#
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
09P C2 C3 SING N N 1
09P C2 N1 SING N N 2
09P C3 C4 SING N N 3
09P N1 C1 SING N N 4
09P C4 N2 SING N N 5
09P C1 C5 SING N N 6
09P C11 C12 SING N N 7
09P C11 O1 SING N N 8
09P N2 C5 SING N N 9
09P N2 C9 SING N N 10
09P C8 C9 DOUB Y N 11
09P C8 C7 SING Y N 12
09P O1 C7 SING N N 13
09P C9 C10 SING Y N 14
09P C7 C6 DOUB Y N 15
09P C10 N3 DOUB Y N 16
09P C6 N3 SING Y N 17
09P C1 H1 SING N N 18
09P C1 H2 SING N N 19
09P N1 H3 SING N N 20
09P C2 H5 SING N N 21
09P C2 H6 SING N N 22
09P C3 H7 SING N N 23
09P C3 H8 SING N N 24
09P C4 H9 SING N N 25
09P C4 H10 SING N N 26
09P C5 H11 SING N N 27
09P C5 H12 SING N N 28
09P C6 H13 SING N N 29
09P C8 H14 SING N N 30
09P C10 H15 SING N N 31
09P C11 H16 SING N N 32
09P C11 H17 SING N N 33
09P C12 H18 SING N N 34
09P C12 H19 SING N N 35
09P C12 H20 SING N N 36
#
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
09P SMILES ACDLabs 12.01 O(c1cc(cnc1)N2CCCNCC2)CC
09P InChI InChI 1.03 InChI=1S/C12H19N3O/c1-2-16-12-8-11(9-14-10-12)15-6-3-4-13-5-7-15/h8-10,13H,2-7H2,1H3
09P InChIKey InChI 1.03 RQXFSCANOMMTFZ-UHFFFAOYSA-N
09P SMILES_CANONICAL CACTVS 3.370 CCOc1cncc(c1)N2CCCNCC2
09P SMILES CACTVS 3.370 CCOc1cncc(c1)N2CCCNCC2
09P SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 CCOc1cc(cnc1)N2CCCNCC2
09P SMILES "OpenEye OEToolkits" 1.7.2 CCOc1cc(cnc1)N2CCCNCC2
#
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
09P "SYSTEMATIC NAME" ACDLabs 12.01 1-(5-ethoxypyridin-3-yl)-1,4-diazepane
09P "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 1-(5-ethoxypyridin-3-yl)-1,4-diazepane
#
_pdbx_chem_comp_audit.comp_id 09P
_pdbx_chem_comp_audit.action_type 'Create component'
_pdbx_chem_comp_audit.date 2011-11-07
_pdbx_chem_comp_audit.processing_site 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
09P C1 C 6.370 3.426 1
09P N1 N 5.435 4.599 2
09P C2 C 3.935 4.599 3
09P C3 C 3.000 3.426 4
09P C4 C 3.334 1.964 5
09P N2 N 4.685 1.313 6
09P C5 C 6.037 1.964 7
09P C6 C 4.685 -3.187 8
09P C7 C 5.984 -2.437 9
09P C8 C 5.984 -0.937 10
09P C9 C 4.685 -0.187 11
09P C10 C 3.386 -0.937 12
09P N3 N 3.386 -2.437 13
09P O1 O 7.283 -3.187 14
09P C11 C 7.283 -4.687 15
09P C12 C 8.582 -5.437 16
#
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
09P C2 C3 SINGLE NONE 1
09P C2 N1 SINGLE NONE 2
09P C3 C4 SINGLE NONE 3
09P N1 C1 SINGLE NONE 4
09P C4 N2 SINGLE NONE 5
09P C1 C5 SINGLE NONE 6
09P C11 C12 SINGLE NONE 7
09P C11 O1 SINGLE NONE 8
09P N2 C5 SINGLE NONE 9
09P N2 C9 SINGLE NONE 10
09P C8 C9 DOUBLE NONE 11
09P C8 C7 SINGLE NONE 12
09P O1 C7 SINGLE NONE 13
09P C9 C10 SINGLE NONE 14
09P C7 C6 DOUBLE NONE 15
09P C10 N3 DOUBLE NONE 16
09P C6 N3 SINGLE NONE 17
#
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
09P MurckoScaffold S1 scaffold c1cncc(N2CCCNCC2)c1 InChI=1S/C10H15N3/c1-3-10(9-12-4-1)13-7-2-5-11-6-8-13/h1,3-4,9,11H,2,5-8H2 JBOVXXZNZSULJJ-UHFFFAOYSA-N
09P 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
09P C1 S1 1
09P N1 S1 1
09P C2 S1 1
09P C3 S1 1
09P C4 S1 1
09P N2 S1 1
09P C5 S1 1
09P C6 S1 1
09P C7 S1 1
09P C8 S1 1
09P C9 S1 1
09P C10 S1 1
09P N3 S1 1
09P C6 F1 1
09P C7 F1 1
09P C8 F1 1
09P C9 F1 1
09P C10 F1 1
09P N3 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 09P
_pdbe_chem_comp_rdkit_properties.exactmw 221.153
_pdbe_chem_comp_rdkit_properties.amw 221.304
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 35
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.583
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_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 123.376
_pdbe_chem_comp_rdkit_properties.tpsa 37.390
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.437
_pdbe_chem_comp_rdkit_properties.CrippenMR 63.672
_pdbe_chem_comp_rdkit_properties.chi0v 7.750
_pdbe_chem_comp_rdkit_properties.chi1v 3.973
_pdbe_chem_comp_rdkit_properties.chi2v 1.425
_pdbe_chem_comp_rdkit_properties.chi3v 1.425
_pdbe_chem_comp_rdkit_properties.chi4v 0.852
_pdbe_chem_comp_rdkit_properties.chi0n 26.750
_pdbe_chem_comp_rdkit_properties.chi1n 13.421
_pdbe_chem_comp_rdkit_properties.chi2n 1.425
_pdbe_chem_comp_rdkit_properties.chi3n 1.425
_pdbe_chem_comp_rdkit_properties.chi4n 0.852
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.290
_pdbe_chem_comp_rdkit_properties.kappa1 2.295
_pdbe_chem_comp_rdkit_properties.kappa2 5.701
_pdbe_chem_comp_rdkit_properties.kappa3 2.854
_pdbe_chem_comp_rdkit_properties.Phi 0.818
#
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
09P UniChem PDBe 09P
09P UniChem SureChEMBL SCHEMBL5657395
09P UniChem PubChem 22053540
09P UniChem BindingDb 92377
#
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
09P C1 -3.274 -0.604 -1.008 ETKDGv3 1
09P N1 -4.387 -0.485 -0.058 ETKDGv3 2
09P C2 -4.276 0.697 0.805 ETKDGv3 3
09P C3 -3.127 0.580 1.820 ETKDGv3 4
09P C4 -1.776 1.023 1.240 ETKDGv3 5
09P N2 -1.234 0.133 0.197 ETKDGv3 6
09P C5 -1.966 -1.032 -0.327 ETKDGv3 7
09P C6 2.713 0.938 -1.148 ETKDGv3 8
09P C7 2.419 -0.298 -0.697 ETKDGv3 9
09P C8 1.042 -0.574 -0.238 ETKDGv3 10
09P C9 0.105 0.389 -0.268 ETKDGv3 11
09P C10 0.485 1.730 -0.767 ETKDGv3 12
09P N3 1.700 1.958 -1.172 ETKDGv3 13
09P O1 3.356 -1.344 -0.647 ETKDGv3 14
09P C11 4.749 -1.235 -0.945 ETKDGv3 15
09P C12 5.494 -0.552 0.197 ETKDGv3 16
09P H1 -3.549 -1.380 -1.756 ETKDGv3 17
09P H2 -3.132 0.344 -1.572 ETKDGv3 18
09P H3 -4.466 -1.352 0.523 ETKDGv3 19
09P H5 -4.179 1.621 0.192 ETKDGv3 20
09P H6 -5.228 0.795 1.370 ETKDGv3 21
09P H7 -3.060 -0.447 2.238 ETKDGv3 22
09P H8 -3.358 1.254 2.674 ETKDGv3 23
09P H9 -1.047 1.069 2.079 ETKDGv3 24
09P H10 -1.878 2.052 0.835 ETKDGv3 25
09P H11 -2.149 -1.768 0.485 ETKDGv3 26
09P H12 -1.352 -1.556 -1.092 ETKDGv3 27
09P H13 3.701 1.190 -1.503 ETKDGv3 28
09P H14 0.802 -1.559 0.142 ETKDGv3 29
09P H15 -0.247 2.525 -0.816 ETKDGv3 30
09P H16 4.910 -0.699 -1.904 ETKDGv3 31
09P H17 5.159 -2.259 -1.066 ETKDGv3 32
09P H18 6.580 -0.519 -0.034 ETKDGv3 33
09P H19 5.344 -1.120 1.139 ETKDGv3 34
09P H20 5.130 0.486 0.340 ETKDGv3 35
#