data_2KU
#
_chem_comp.id 2KU
_chem_comp.name N-(3-METHOXYPROPYL)-9H-PURIN-6-AMINE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type ?
_chem_comp.formula "C9 H13 N5 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2011-03-25
_chem_comp.pdbx_modified_date 2011-06-10
_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 207.232
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 2KU
_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 2YEH
_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
2KU C15 C15 C 0 1 N N N N N N 34.004 7.513 23.417 6.483 0.025 -0.000 C15 2KU 1
2KU C13 C13 C 0 1 N N N N N N 34.856 9.692 23.411 4.097 0.253 -0.000 C13 2KU 2
2KU C12 C12 C 0 1 N N N N N N 34.359 11.128 23.592 2.801 -0.559 0.000 C12 2KU 3
2KU C11 C11 C 0 1 N N N N N N 32.855 11.155 23.874 1.603 0.393 -0.000 C11 2KU 4
2KU N1 N1 N 0 1 Y N N N N N 31.205 9.698 26.721 -0.927 1.590 -0.000 N1 2KU 5
2KU C2 C2 C 0 1 Y N N N N N 30.020 9.703 27.319 -2.089 2.218 -0.001 C2 2KU 6
2KU N3 N3 N 0 1 Y N N N N N 28.929 10.125 26.692 -3.239 1.576 -0.001 N3 2KU 7
2KU C4 C4 C 0 1 Y N N N N N 28.998 10.559 25.427 -3.273 0.247 -0.001 C4 2KU 8
2KU C5 C5 C 0 1 Y N N N N N 30.211 10.567 24.779 -2.062 -0.467 -0.000 C5 2KU 9
2KU C6 C6 C 0 1 Y N N N N N 31.333 10.122 25.455 -0.862 0.263 -0.000 C6 2KU 10
2KU N10 N10 N 0 1 N N N N N N 32.521 10.116 24.858 0.361 -0.385 0.000 N10 2KU 11
2KU N7 N7 N 0 1 Y N N N N N 30.011 11.037 23.554 -2.376 -1.785 0.001 N7 2KU 12
2KU C8 C8 C 0 1 Y N N N N N 28.711 11.319 23.430 -3.671 -1.922 0.001 C8 2KU 13
2KU N9 N9 N 0 1 Y N N N N N 28.091 11.026 24.577 -4.268 -0.697 0.001 N9 2KU 14
2KU O12 O12 O 0 1 N N N N N N 33.768 8.857 22.989 5.216 -0.636 0.000 O12 2KU 15
2KU H151 H151 H 0 0 N N N N N N 33.170 6.873 23.094 6.568 0.649 0.890 H151 2KU 16
2KU H152 H152 H 0 0 N N N N N N 34.941 7.146 22.973 7.280 -0.719 0.000 H152 2KU 17
2KU H153 H153 H 0 0 N N N N N N 34.083 7.486 24.514 6.568 0.648 -0.890 H153 2KU 18
2KU H131 H131 H 0 0 N N N N N N 35.649 9.672 22.649 4.132 0.881 -0.890 H131 2KU 19
2KU H132 H132 H 0 0 N N N N N N 35.255 9.319 24.366 4.132 0.882 0.890 H132 2KU 20
2KU H121 H121 H 0 0 N N N N N N 34.890 11.586 24.439 2.766 -1.188 -0.890 H121 2KU 21
2KU H122 H122 H 0 0 N N N N N N 34.561 11.695 22.671 2.766 -1.187 0.890 H122 2KU 22
2KU H111 H111 H 0 0 N N N N N N 32.575 12.141 24.273 1.638 1.021 0.890 H111 2KU 23
2KU H112 H112 H 0 0 N N N N N N 32.304 10.967 22.941 1.638 1.021 -0.890 H112 2KU 24
2KU H10 H10 H 0 1 N N N N N N 32.583 9.244 24.372 0.396 -1.355 0.000 H10 2KU 25
2KU H2 H2 H 0 1 N N N N N N 29.942 9.356 28.339 -2.097 3.297 -0.001 H2 2KU 26
2KU H9 H9 H 0 1 N N N N N N 27.115 11.139 24.763 -5.223 -0.524 0.001 H9 2KU 27
2KU H8 H8 H 0 1 N N N N N N 28.238 11.719 22.546 -4.194 -2.866 0.002 H8 2KU 28
#
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
2KU C15 O12 SING N N 1
2KU C13 C12 SING N N 2
2KU C13 O12 SING N N 3
2KU C12 C11 SING N N 4
2KU C11 N10 SING N N 5
2KU N1 C2 SING Y N 6
2KU N1 C6 DOUB Y N 7
2KU C2 N3 DOUB Y N 8
2KU N3 C4 SING Y N 9
2KU C4 C5 DOUB Y N 10
2KU C4 N9 SING Y N 11
2KU C5 C6 SING Y N 12
2KU C5 N7 SING Y N 13
2KU C6 N10 SING N N 14
2KU N7 C8 DOUB Y N 15
2KU C8 N9 SING Y N 16
2KU C15 H151 SING N N 17
2KU C15 H152 SING N N 18
2KU C15 H153 SING N N 19
2KU C13 H131 SING N N 20
2KU C13 H132 SING N N 21
2KU C12 H121 SING N N 22
2KU C12 H122 SING N N 23
2KU C11 H111 SING N N 24
2KU C11 H112 SING N N 25
2KU N10 H10 SING N N 26
2KU C2 H2 SING N N 27
2KU N9 H9 SING N N 28
2KU C8 H8 SING N N 29
#
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
2KU SMILES ACDLabs 12.01 n2c1c(ncn1)c(nc2)NCCCOC
2KU SMILES_CANONICAL CACTVS 3.370 COCCCNc1ncnc2[nH]cnc12
2KU SMILES CACTVS 3.370 COCCCNc1ncnc2[nH]cnc12
2KU SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 COCCCNc1c2c([nH]cn2)ncn1
2KU SMILES "OpenEye OEToolkits" 1.7.0 COCCCNc1c2c([nH]cn2)ncn1
2KU InChI InChI 1.03 InChI=1S/C9H13N5O/c1-15-4-2-3-10-8-7-9(12-5-11-7)14-6-13-8/h5-6H,2-4H2,1H3,(H2,10,11,12,13,14)
2KU InChIKey InChI 1.03 BUGJFSHIPBSLKT-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
2KU "SYSTEMATIC NAME" ACDLabs 12.01 N-(3-methoxypropyl)-9H-purin-6-amine
2KU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 N-(3-methoxypropyl)-9H-purin-6-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
2KU 'Create component' 2011-03-25 EBI
2KU 'Modify aromatic_flag' 2011-06-04 RCSB
2KU '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
2KU C15 C 3.000 4.875 1
2KU C13 C 4.299 2.625 2
2KU C12 C 5.598 1.875 3
2KU C11 C 5.598 0.375 4
2KU N1 N 5.598 -2.625 5
2KU C2 C 5.598 -4.125 6
2KU N3 N 6.897 -4.875 7
2KU C4 C 8.196 -4.125 8
2KU C5 C 8.196 -2.625 9
2KU C6 C 6.897 -1.875 10
2KU N10 N 6.897 -0.375 11
2KU N7 N 9.616 -2.168 12
2KU C8 C 10.491 -3.375 13
2KU N9 N 9.616 -4.582 14
2KU O12 O 4.299 4.125 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
2KU C15 O12 SINGLE NONE 1
2KU C13 C12 SINGLE NONE 2
2KU C13 O12 SINGLE NONE 3
2KU C12 C11 SINGLE NONE 4
2KU C11 N10 SINGLE NONE 5
2KU N1 C2 DOUBLE NONE 6
2KU N1 C6 SINGLE NONE 7
2KU C2 N3 SINGLE NONE 8
2KU N3 C4 DOUBLE NONE 9
2KU C4 C5 SINGLE NONE 10
2KU C4 N9 SINGLE NONE 11
2KU C5 C6 DOUBLE NONE 12
2KU C5 N7 SINGLE NONE 13
2KU C6 N10 SINGLE NONE 14
2KU N7 C8 DOUBLE NONE 15
2KU C8 N9 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
2KU MurckoScaffold S1 scaffold 'c1ncc2nc[nH]c2n1' InChI=1S/C5H4N4/c1-4-5(8-2-6-1)9-3-7-4/h1-3H,(H,6,7,8,9) KDCGOANMDULRCW-UHFFFAOYSA-N
2KU adenine F1 fragment 'Nc1ncnc2nc[nH]c12' InChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10) GFFGJBXGBJISGV-UHFFFAOYSA-N
2KU imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
2KU purine F3 fragment 'c1ncc2[nH]cnc2n1' InChI=1S/C5H4N4/c1-4-5(8-2-6-1)9-3-7-4/h1-3H,(H,6,7,8,9) KDCGOANMDULRCW-UHFFFAOYSA-N
2KU pyrimidine F4 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-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
2KU N1 S1 1
2KU C2 S1 1
2KU N3 S1 1
2KU C4 S1 1
2KU C5 S1 1
2KU C6 S1 1
2KU N7 S1 1
2KU C8 S1 1
2KU N9 S1 1
2KU N1 F1 1
2KU C6 F1 1
2KU C5 F1 1
2KU C4 F1 1
2KU N3 F1 1
2KU C2 F1 1
2KU N9 F1 1
2KU C8 F1 1
2KU N7 F1 1
2KU N10 F1 1
2KU C4 F2 1
2KU C5 F2 1
2KU N7 F2 1
2KU C8 F2 1
2KU N9 F2 1
2KU N7 F3 1
2KU C8 F3 1
2KU N9 F3 1
2KU C4 F3 1
2KU C5 F3 1
2KU C6 F3 1
2KU N1 F3 1
2KU C2 F3 1
2KU N3 F3 1
2KU C5 F4 1
2KU C4 F4 1
2KU N3 F4 1
2KU C2 F4 1
2KU N1 F4 1
2KU C6 F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 2KU
_pdbe_chem_comp_rdkit_properties.exactmw 207.112
_pdbe_chem_comp_rdkit_properties.amw 207.237
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 28
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.444
_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 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 105.485
_pdbe_chem_comp_rdkit_properties.tpsa 75.720
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.008
_pdbe_chem_comp_rdkit_properties.CrippenMR 53.636
_pdbe_chem_comp_rdkit_properties.chi0v 7.144
_pdbe_chem_comp_rdkit_properties.chi1v 3.644
_pdbe_chem_comp_rdkit_properties.chi2v 1.373
_pdbe_chem_comp_rdkit_properties.chi3v 1.373
_pdbe_chem_comp_rdkit_properties.chi4v 0.833
_pdbe_chem_comp_rdkit_properties.chi0n 20.144
_pdbe_chem_comp_rdkit_properties.chi1n 10.039
_pdbe_chem_comp_rdkit_properties.chi2n 1.373
_pdbe_chem_comp_rdkit_properties.chi3n 1.373
_pdbe_chem_comp_rdkit_properties.chi4n 0.833
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.690
_pdbe_chem_comp_rdkit_properties.kappa1 2.704
_pdbe_chem_comp_rdkit_properties.kappa2 4.697
_pdbe_chem_comp_rdkit_properties.kappa3 2.214
_pdbe_chem_comp_rdkit_properties.Phi 0.847
#
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
2KU UniChem ChEMBL CHEMBL1488445
2KU UniChem PDBe 2KU
2KU UniChem ZINC ZINC000002719608
2KU UniChem eMolecules 30413214
2KU UniChem eMolecules 4934145
2KU UniChem 'EPA CompTox Dashboard' DTXSID70879568
2KU UniChem SureChEMBL SCHEMBL21153504
2KU UniChem PubChem 2155044
2KU UniChem Mcule MCULE-1296213246
#
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
2KU C15 4.614 -1.078 0.339 ETKDGv3 1
2KU C13 3.424 0.698 -0.568 ETKDGv3 2
2KU C12 2.112 0.905 0.199 ETKDGv3 3
2KU C11 0.925 0.239 -0.508 ETKDGv3 4
2KU N1 -1.641 -0.831 -1.463 ETKDGv3 5
2KU C2 -2.783 -1.314 -1.897 ETKDGv3 6
2KU N3 -4.009 -1.070 -1.167 ETKDGv3 7
2KU C4 -3.924 -0.364 -0.083 ETKDGv3 8
2KU C5 -2.707 0.167 0.406 ETKDGv3 9
2KU C6 -1.566 -0.044 -0.249 ETKDGv3 10
2KU N10 -0.318 0.481 0.222 ETKDGv3 11
2KU N7 -2.967 0.884 1.605 ETKDGv3 12
2KU C8 -4.257 0.773 1.796 ETKDGv3 13
2KU N9 -4.960 0.009 0.797 ETKDGv3 14
2KU O12 3.731 -0.680 -0.686 ETKDGv3 15
2KU H151 4.763 -2.175 0.272 ETKDGv3 16
2KU H152 4.198 -0.856 1.347 ETKDGv3 17
2KU H153 5.608 -0.594 0.214 ETKDGv3 18
2KU H131 3.307 1.114 -1.591 ETKDGv3 19
2KU H132 4.236 1.295 -0.088 ETKDGv3 20
2KU H121 1.919 1.996 0.283 ETKDGv3 21
2KU H122 2.211 0.494 1.227 ETKDGv3 22
2KU H111 1.098 -0.857 -0.574 ETKDGv3 23
2KU H112 0.829 0.649 -1.536 ETKDGv3 24
2KU H10 -0.303 1.044 1.104 ETKDGv3 25
2KU H2 -2.808 -1.898 -2.807 ETKDGv3 26
2KU H9 -5.979 -0.211 0.740 ETKDGv3 27
2KU H8 -4.754 1.223 2.645 ETKDGv3 28
#