data_YHF # _chem_comp.id YHF _chem_comp.name "5'-O-[(S)-(cyclopentyloxy)(hydroxy)phosphoryl]adenosine" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H22 N5 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-02-03 _chem_comp.pdbx_modified_date 2023-02-10 _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 415.338 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YHF _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 8G0R _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.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 YHF C1 C1 C 0 1 N N S -15.584 16.880 19.200 1.071 2.898 -0.256 C1 YHF 1 YHF C10 C2 C 0 1 N N N -15.424 14.380 18.634 -1.176 1.802 -0.519 C10 YHF 2 YHF C11 C3 C 0 1 N N N -13.103 11.509 18.740 -5.613 -1.002 0.035 C11 YHF 3 YHF C12 C4 C 0 1 N N N -11.682 12.115 18.715 -5.534 -2.549 0.046 C12 YHF 4 YHF C13 C5 C 0 1 N N N -11.007 11.692 20.029 -7.011 -2.966 0.249 C13 YHF 5 YHF C14 C6 C 0 1 N N N -12.080 11.096 20.877 -7.568 -1.920 1.236 C14 YHF 6 YHF C15 C7 C 0 1 N N N -13.374 11.625 20.248 -6.679 -0.671 1.100 C15 YHF 7 YHF C2 C8 C 0 1 N N R -15.978 17.573 20.496 2.355 2.062 -0.478 C2 YHF 8 YHF C3 C9 C 0 1 N N R -15.606 16.533 21.538 2.146 0.880 0.503 C3 YHF 9 YHF C4 C10 C 0 1 Y N N -13.149 15.761 21.849 2.439 -1.325 -0.687 C4 YHF 10 YHF C5 C11 C 0 1 Y N N -12.411 17.253 23.204 4.519 -1.778 -0.276 C5 YHF 11 YHF C6 C12 C 0 1 Y N N -13.736 17.566 22.961 4.227 -0.552 0.344 C6 YHF 12 YHF C7 C13 C 0 1 Y N N -13.663 19.328 24.273 6.392 -0.443 1.109 C7 YHF 13 YHF C8 C14 C 0 1 Y N N -11.702 18.103 24.077 5.822 -2.290 -0.152 C8 YHF 14 YHF C9 C15 C 0 1 N N R -16.029 15.443 19.510 0.072 1.900 0.361 C9 YHF 15 YHF N1 N1 N 0 1 Y N N -14.224 16.612 22.094 2.909 -0.292 0.068 N1 YHF 16 YHF N2 N2 N 0 1 Y N N -12.052 16.120 22.503 3.385 -2.196 -0.887 N2 YHF 17 YHF N3 N3 N 0 1 Y N N -14.430 18.595 23.466 5.185 0.075 1.020 N3 YHF 18 YHF N4 N4 N 0 1 Y N N -12.377 19.155 24.604 6.714 -1.592 0.543 N4 YHF 19 YHF N5 N5 N 0 1 N N N -10.422 17.930 24.405 6.168 -3.494 -0.741 N5 YHF 20 YHF O1 O1 O 0 1 N N N -16.235 17.362 18.035 1.326 3.975 0.649 O1 YHF 21 YHF O2 O2 O 0 1 N N N -15.660 15.256 20.889 0.728 0.623 0.423 O2 YHF 22 YHF O3 O3 O 0 1 N N N -17.384 17.788 20.567 3.519 2.814 -0.131 O3 YHF 23 YHF O4 O4 O 0 1 N N N -15.987 13.098 18.967 -2.143 0.966 0.118 O4 YHF 24 YHF O5 O5 O 0 1 N N N -16.150 12.153 16.645 -3.398 0.081 -1.885 O5 YHF 25 YHF O6 O6 O 0 1 N N N -13.977 12.233 17.928 -4.354 -0.431 0.394 O6 YHF 26 YHF O7 O7 O 0 1 N N N -15.833 10.621 18.677 -4.449 1.994 -0.617 O7 YHF 27 YHF P1 P1 P 0 1 N N N -15.550 11.914 17.987 -3.582 0.640 -0.527 P1 YHF 28 YHF H1 H1 H 0 1 N N N -14.491 16.908 19.083 0.694 3.278 -1.206 H1 YHF 29 YHF H2 H2 H 0 1 N N N -14.336 14.353 18.791 -1.596 2.797 -0.666 H2 YHF 30 YHF H3 H3 H 0 1 N N N -15.637 14.610 17.580 -0.906 1.375 -1.485 H3 YHF 31 YHF H4 H4 H 0 1 N N N -13.058 10.449 18.451 -5.929 -0.643 -0.945 H4 YHF 32 YHF H5 H5 H 0 1 N N N -11.118 11.726 17.855 -5.153 -2.923 -0.904 H5 YHF 33 YHF H6 H6 H 0 1 N N N -11.737 13.212 18.651 -4.917 -2.898 0.875 H6 YHF 34 YHF H7 H7 H 0 1 N N N -10.221 10.949 19.831 -7.552 -2.925 -0.697 H7 YHF 35 YHF H8 H8 H 0 1 N N N -10.567 12.567 20.530 -7.070 -3.966 0.679 H8 YHF 36 YHF H9 H9 H 0 1 N N N -12.046 9.997 20.839 -8.599 -1.674 0.978 H9 YHF 37 YHF H10 H10 H 0 1 N N N -11.986 11.430 21.921 -7.520 -2.304 2.254 H10 YHF 38 YHF H11 H11 H 0 1 N N N -13.555 12.671 20.537 -6.199 -0.449 2.053 H11 YHF 39 YHF H12 H12 H 0 1 N N N -14.236 11.009 20.542 -7.278 0.180 0.776 H12 YHF 40 YHF H13 H13 H 0 1 N N N -15.402 18.499 20.639 2.415 1.708 -1.507 H13 YHF 41 YHF H14 H14 H 0 1 N N N -16.334 16.573 22.361 2.430 1.167 1.515 H14 YHF 42 YHF H15 H15 H 0 1 N N N -13.203 14.902 21.197 1.429 -1.411 -1.060 H15 YHF 43 YHF H16 H16 H 0 1 N N N -14.147 20.182 24.723 7.148 0.092 1.665 H16 YHF 44 YHF H17 H17 H 0 1 N N N -17.124 15.395 19.414 -0.206 2.226 1.363 H17 YHF 45 YHF H18 H18 H 0 1 N N N -10.138 18.654 25.033 5.508 -3.994 -1.246 H18 YHF 46 YHF H19 H19 H 0 1 N N N -10.309 17.041 24.848 7.071 -3.837 -0.648 H19 YHF 47 YHF H20 H20 H 0 1 N N N -15.950 18.250 17.857 1.948 4.633 0.311 H20 YHF 48 YHF H21 H21 H 0 1 N N N -17.598 18.221 21.385 3.643 3.614 -0.660 H21 YHF 49 YHF H22 H22 H 0 1 N N N -16.397 10.087 18.130 -4.609 2.416 0.238 H22 YHF 50 # 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 YHF O5 P1 DOUB N N 1 YHF O6 P1 SING N N 2 YHF O6 C11 SING N N 3 YHF P1 O7 SING N N 4 YHF P1 O4 SING N N 5 YHF O1 C1 SING N N 6 YHF C10 O4 SING N N 7 YHF C10 C9 SING N N 8 YHF C12 C11 SING N N 9 YHF C12 C13 SING N N 10 YHF C11 C15 SING N N 11 YHF C1 C9 SING N N 12 YHF C1 C2 SING N N 13 YHF C9 O2 SING N N 14 YHF C13 C14 SING N N 15 YHF C15 C14 SING N N 16 YHF C2 O3 SING N N 17 YHF C2 C3 SING N N 18 YHF O2 C3 SING N N 19 YHF C3 N1 SING N N 20 YHF C4 N1 SING Y N 21 YHF C4 N2 DOUB Y N 22 YHF N1 C6 SING Y N 23 YHF N2 C5 SING Y N 24 YHF C6 C5 DOUB Y N 25 YHF C6 N3 SING Y N 26 YHF C5 C8 SING Y N 27 YHF N3 C7 DOUB Y N 28 YHF C8 N5 SING N N 29 YHF C8 N4 DOUB Y N 30 YHF C7 N4 SING Y N 31 YHF C1 H1 SING N N 32 YHF C10 H2 SING N N 33 YHF C10 H3 SING N N 34 YHF C11 H4 SING N N 35 YHF C12 H5 SING N N 36 YHF C12 H6 SING N N 37 YHF C13 H7 SING N N 38 YHF C13 H8 SING N N 39 YHF C14 H9 SING N N 40 YHF C14 H10 SING N N 41 YHF C15 H11 SING N N 42 YHF C15 H12 SING N N 43 YHF C2 H13 SING N N 44 YHF C3 H14 SING N N 45 YHF C4 H15 SING N N 46 YHF C7 H16 SING N N 47 YHF C9 H17 SING N N 48 YHF N5 H18 SING N N 49 YHF N5 H19 SING N N 50 YHF O1 H20 SING N N 51 YHF O3 H21 SING N N 52 YHF O7 H22 SING N N 53 # 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 YHF SMILES ACDLabs 12.01 "O=P(O)(OC1CCCC1)OCC1OC(n2cnc3c(N)ncnc32)C(O)C1O" YHF InChI InChI 1.06 "InChI=1S/C15H22N5O7P/c16-13-10-14(18-6-17-13)20(7-19-10)15-12(22)11(21)9(26-15)5-25-28(23,24)27-8-3-1-2-4-8/h6-9,11-12,15,21-22H,1-5H2,(H,23,24)(H2,16,17,18)/t9-,11-,12-,15-/m1/s1" YHF InChIKey InChI 1.06 ILDPDEYZUPQLBS-SDBHATRESA-N YHF SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)OC4CCCC4)[C@@H](O)[C@H]3O" YHF SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)OC4CCCC4)[CH](O)[CH]3O" YHF SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OC4CCCC4)O)O)N" YHF SMILES "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OC4CCCC4)O)O)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 YHF "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(S)-(cyclopentyloxy)(hydroxy)phosphoryl]adenosine" YHF "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl cyclopentyl hydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YHF "Create component" 2023-02-03 RCSB YHF "Initial release" 2023-02-15 RCSB #