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 
# 
