data_YCX
# 
_chem_comp.id                                    YCX 
_chem_comp.name                                  "[[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-2,3,4,5,6-pentakis(oxidanyl)hexyl] hydrogen phosphate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C15 H27 N3 O16 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-12-01 
_chem_comp.pdbx_modified_date                    2023-12-15 
_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                        567.333 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YCX 
_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        8V4H 
_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_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_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 
YCX N1    N1  N 0 1 N N N N N N -8.466  1.364  -11.601 5.999   1.716  -0.490 N1    YCX 1  
YCX N3    N2  N 0 1 N N N N N N -6.896  2.598  -12.846 6.782   2.546  1.544  N3    YCX 2  
YCX C4    C1  C 0 1 N N N N N N -7.043  3.568  -11.927 7.004   3.736  1.001  C4    YCX 3  
YCX C5    C2  C 0 1 N N N N N N -7.840  3.442  -10.891 6.717   3.944  -0.363 C5    YCX 4  
YCX C6    C3  C 0 1 N N N N N N -8.544  2.375  -10.716 6.214   2.919  -1.092 C6    YCX 5  
YCX O2B   O1  O 0 1 N N N N N N -10.281 -1.609 -6.045  -2.374  -2.685 1.771  O2B   YCX 6  
YCX PB    P1  P 0 1 N N N N N N -10.570 -0.531 -5.062  -1.973  -1.352 1.269  PB    YCX 7  
YCX O1B   O2  O 0 1 N N N N N N -9.590  -0.544 -3.967  -1.738  -0.358 2.514  O1B   YCX 8  
YCX O6G   O3  O 0 1 N N N N N N -12.045 -0.646 -4.477  -3.134  -0.762 0.323  O6G   YCX 9  
YCX C6G   C4  C 0 1 N N N N N N -12.405 0.327  -3.487  -4.491  -0.624 0.751  C6G   YCX 10 
YCX C5G   C5  C 0 1 N N R N N N -13.908 0.238  -3.179  -5.327  -0.036 -0.388 C5G   YCX 11 
YCX O5G   O4  O 0 1 N N N N N N -14.371 -1.087 -2.810  -5.366  -0.960 -1.477 O5G   YCX 12 
YCX C4G   C6  C 0 1 N N R N N N -14.238 1.247  -2.073  -6.750  0.228  0.108  C4G   YCX 13 
YCX O4G   O5  O 0 1 N N N N N N -13.833 2.508  -2.554  -6.711  1.153  1.198  O4G   YCX 14 
YCX C3G   C7  C 0 1 N N R N N N -15.672 1.381  -1.756  -7.586  0.817  -1.030 C3G   YCX 15 
YCX O3G   O6  O 0 1 N N N N N N -16.483 1.529  -2.934  -6.937  1.981  -1.545 O3G   YCX 16 
YCX C2G   C8  C 0 1 N N S N N N -15.922 2.609  -0.903  -8.971  1.197  -0.502 C2G   YCX 17 
YCX O2G   O7  O 0 1 N N N N N N -17.334 2.624  -0.668  -8.830  2.077  0.615  O2G   YCX 18 
YCX C1G   C9  C 0 1 N N N N N N -15.127 2.632  0.369   -9.763  1.899  -1.607 C1G   YCX 19 
YCX O1G   O8  O 0 1 N N N N N N -15.412 3.807  1.143   -11.094 2.149  -1.153 O1G   YCX 20 
YCX O3B   O9  O 0 1 N N N N N N -10.277 0.935  -5.676  -0.609  -1.485 0.424  O3B   YCX 21 
YCX PA    P2  P 0 1 N N N N N N -11.168 1.790  -6.687  0.745   -2.337 0.612  PA    YCX 22 
YCX O1A   O10 O 0 1 N N N N N N -12.630 1.733  -6.509  1.126   -2.348 2.042  O1A   YCX 23 
YCX O2A   O11 O 0 1 N N N N N N -10.819 3.205  -6.485  0.502   -3.848 0.110  O2A   YCX 24 
YCX "O5'" O12 O 0 1 N N N N N N -10.904 1.353  -8.183  1.925   -1.667 -0.253 "O5'" YCX 25 
YCX "C5'" C10 C 0 1 N N N N N N -11.705 0.331  -8.752  3.277   -2.129 -0.215 "C5'" YCX 26 
YCX "C4'" C11 C 0 1 N N R N N N -10.847 -0.398 -9.742  4.134   -1.275 -1.151 "C4'" YCX 27 
YCX "C3'" C12 C 0 1 N N S N N N -9.478  -0.801 -9.254  5.573   -1.834 -1.222 "C3'" YCX 28 
YCX "O3'" O13 O 0 1 N N N N N N -9.501  -1.996 -8.459  5.741   -2.637 -2.391 "O3'" YCX 29 
YCX "C2'" C13 C 0 1 N N R N N N -8.704  -0.919 -10.559 6.462   -0.572 -1.300 "C2'" YCX 30 
YCX "O2'" O14 O 0 1 N N N N N N -9.034  -2.115 -11.186 7.209   -0.560 -2.518 "O2'" YCX 31 
YCX "C1'" C14 C 0 1 N N R N N N -9.288  0.139  -11.446 5.456   0.599  -1.266 "C1'" YCX 32 
YCX "O4'" O15 O 0 1 N N N N N N -10.548 0.472  -10.824 4.283   0.060  -0.619 "O4'" YCX 33 
YCX N4    N3  N 0 1 N N N N N N -6.308  4.691  -12.110 7.515   4.760  1.765  N4    YCX 34 
YCX C2    C15 C 0 1 N N N N N N -7.586  1.497  -12.707 6.287   1.547  0.814  C2    YCX 35 
YCX O2    O16 O 0 1 N N N N N N -7.455  0.642  -13.580 6.093   0.462  1.336  O2    YCX 36 
YCX H1    H1  H 0 1 N N N N N N -7.907  4.246  -10.173 6.892   4.907  -0.820 H1    YCX 37 
YCX H2    H2  H 0 1 N N N N N N -9.196  2.293  -9.859  5.987   3.054  -2.139 H2    YCX 38 
YCX H3    H3  H 0 1 N N N N N N -8.964  -1.245 -4.110  -1.472  0.536  2.259  H3    YCX 39 
YCX H4    H4  H 0 1 N N N N N N -11.833 0.138  -2.566  -4.887  -1.602 1.024  H4    YCX 40 
YCX H5    H5  H 0 1 N N N N N N -12.170 1.333  -3.864  -4.534  0.040  1.614  H5    YCX 41 
YCX H6    H6  H 0 1 N N N N N N -14.447 0.554  -4.084  -4.879  0.900  -0.721 H6    YCX 42 
YCX H7    H7  H 0 1 N N N N N N -15.305 -1.060 -2.636  -5.753  -1.817 -1.252 H7    YCX 43 
YCX H8    H8  H 0 1 N N N N N N -13.679 0.978  -1.164  -7.198  -0.707 0.442  H8    YCX 44 
YCX H9    H9  H 0 1 N N N N N N -14.018 3.171  -1.900  -6.323  2.010  0.973  H9    YCX 45 
YCX H10   H10 H 0 1 N N N N N N -15.999 0.494  -1.194  -7.690  0.078  -1.824 H10   YCX 46 
YCX H11   H11 H 0 1 N N N N N N -17.395 1.612  -2.683  -6.810  2.683  -0.891 H11   YCX 47 
YCX H12   H12 H 0 1 N N N N N N -15.647 3.495  -1.495  -9.500  0.296  -0.191 H12   YCX 48 
YCX H13   H13 H 0 1 N N N N N N -17.559 3.377  -0.134  -8.366  2.900  0.411  H13   YCX 49 
YCX H14   H14 H 0 1 N N N N N N -15.378 1.742  0.964   -9.280  2.844  -1.856 H14   YCX 50 
YCX H15   H15 H 0 1 N N N N N N -14.055 2.617  0.122   -9.794  1.263  -2.492 H15   YCX 51 
YCX H16   H16 H 0 1 N N N N N N -14.896 3.794  1.940   -11.655 2.593  -1.804 H16   YCX 52 
YCX H17   H17 H 0 1 N N N N N N -11.606 3.702  -6.297  0.249   -3.917 -0.820 H17   YCX 53 
YCX H18   H18 H 0 1 N N N N N N -12.576 0.772  -9.259  3.660   -2.049 0.803  H18   YCX 54 
YCX H19   H19 H 0 1 N N N N N N -12.048 -0.360 -7.968  3.314   -3.170 -0.536 H19   YCX 55 
YCX H20   H20 H 0 1 N N N N N N -11.381 -1.290 -10.101 3.691   -1.241 -2.146 H20   YCX 56 
YCX H21   H21 H 0 1 N N N N N N -9.053  0.027  -8.668  5.803   -2.411 -0.326 H21   YCX 57 
YCX H22   H22 H 0 1 N N N N N N -9.797  -1.787 -7.581  6.626   -3.014 -2.486 H22   YCX 58 
YCX H23   H23 H 0 1 N N N N N N -7.624  -0.780 -10.406 7.133   -0.524 -0.442 H23   YCX 59 
YCX H24   H24 H 0 1 N N N N N N -8.695  -2.843 -10.679 7.813   -1.309 -2.616 H24   YCX 60 
YCX H25   H25 H 0 1 N N N N N N -9.473  -0.295 -12.440 5.215   0.924  -2.279 H25   YCX 61 
YCX H26   H26 H 0 1 N N N N N N -5.696  4.765  -12.898 7.714   4.612  2.703  H26   YCX 62 
YCX H27   H27 H 0 1 N N N N N N -6.377  5.446  -11.457 7.676   5.629  1.366  H27   YCX 63 
# 
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 
YCX O2    C2    DOUB N N 1  
YCX N3    C2    SING N N 2  
YCX N3    C4    DOUB N N 3  
YCX C2    N1    SING N N 4  
YCX N4    C4    SING N N 5  
YCX C4    C5    SING N N 6  
YCX N1    "C1'" SING N N 7  
YCX N1    C6    SING N N 8  
YCX "C1'" "O4'" SING N N 9  
YCX "C1'" "C2'" SING N N 10 
YCX "O2'" "C2'" SING N N 11 
YCX C5    C6    DOUB N N 12 
YCX "O4'" "C4'" SING N N 13 
YCX "C2'" "C3'" SING N N 14 
YCX "C4'" "C3'" SING N N 15 
YCX "C4'" "C5'" SING N N 16 
YCX "C3'" "O3'" SING N N 17 
YCX "C5'" "O5'" SING N N 18 
YCX "O5'" PA    SING N N 19 
YCX PA    O1A   DOUB N N 20 
YCX PA    O2A   SING N N 21 
YCX PA    O3B   SING N N 22 
YCX O2B   PB    DOUB N N 23 
YCX O3B   PB    SING N N 24 
YCX PB    O6G   SING N N 25 
YCX PB    O1B   SING N N 26 
YCX O6G   C6G   SING N N 27 
YCX C6G   C5G   SING N N 28 
YCX C5G   O5G   SING N N 29 
YCX C5G   C4G   SING N N 30 
YCX O3G   C3G   SING N N 31 
YCX O4G   C4G   SING N N 32 
YCX C4G   C3G   SING N N 33 
YCX C3G   C2G   SING N N 34 
YCX C2G   O2G   SING N N 35 
YCX C2G   C1G   SING N N 36 
YCX C1G   O1G   SING N N 37 
YCX C5    H1    SING N N 38 
YCX C6    H2    SING N N 39 
YCX O1B   H3    SING N N 40 
YCX C6G   H4    SING N N 41 
YCX C6G   H5    SING N N 42 
YCX C5G   H6    SING N N 43 
YCX O5G   H7    SING N N 44 
YCX C4G   H8    SING N N 45 
YCX O4G   H9    SING N N 46 
YCX C3G   H10   SING N N 47 
YCX O3G   H11   SING N N 48 
YCX C2G   H12   SING N N 49 
YCX O2G   H13   SING N N 50 
YCX C1G   H14   SING N N 51 
YCX C1G   H15   SING N N 52 
YCX O1G   H16   SING N N 53 
YCX O2A   H17   SING N N 54 
YCX "C5'" H18   SING N N 55 
YCX "C5'" H19   SING N N 56 
YCX "C4'" H20   SING N N 57 
YCX "C3'" H21   SING N N 58 
YCX "O3'" H22   SING N N 59 
YCX "C2'" H23   SING N N 60 
YCX "O2'" H24   SING N N 61 
YCX "C1'" H25   SING N N 62 
YCX N4    H26   SING N N 63 
YCX N4    H27   SING N N 64 
# 
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 
YCX SMILES           ACDLabs              12.01 "OCC(O)C(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC1OC(N2C=CC(N)=NC2=O)C(O)C1O"                                                                                                                                                             
YCX InChI            InChI                1.06  "InChI=1S/C15H27N3O16P2/c16-9-1-2-18(15(26)17-9)14-13(25)12(24)8(33-14)5-32-36(29,30)34-35(27,28)31-4-7(21)11(23)10(22)6(20)3-19/h1-2,6-8,10-14,19-25H,3-5H2,(H,27,28)(H,29,30)(H2,16,17,26)/t6-,7+,8+,10+,11+,12+,13+,14+/m0/s1" 
YCX InChIKey         InChI                1.06  WSJYSDVJOUCAAL-WZWGQWAVSA-N                                                                                                                                                                                                       
YCX SMILES_CANONICAL CACTVS               3.385 "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)CO)[C@@H](O)[C@H]2O"                                                                                                                  
YCX SMILES           CACTVS               3.385 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH](O)[CH](O)[CH](O)[CH](O)CO)[CH](O)[CH]2O"                                                                                                                               
YCX SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OC[C@H]([C@H]([C@@H]([C@H](CO)O)O)O)O)O)O"                                                                                                                      
YCX SMILES           "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCC(C(C(C(CO)O)O)O)O)O)O"                                                                                                                                                         
# 
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 
YCX "SYSTEMATIC NAME" ACDLabs              12.01 "[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3R,4R,5S)-2,3,4,5,6-pentahydroxyhexyl dihydrogen diphosphate (non-preferred name)"                                           
YCX "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-2,3,4,5,6-pentakis(oxidanyl)hexyl] 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 
YCX "Create component" 2023-12-01 RCSB 
YCX "Initial release"  2023-12-20 RCSB 
# 
