data_Y4I
# 
_chem_comp.id                                    Y4I 
_chem_comp.name                                  "1-[(2~{R},4~{S},5~{R})-5-[[[(2~{R},6~{S})-2-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-6-(hydroxymethyl)morpholin-4-yl]-oxidanyl-phosphinothioyl]oxymethyl]-4-oxidanyl-oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C19 H26 N5 O10 P S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-11-20 
_chem_comp.pdbx_modified_date                    2023-12-01 
_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                        547.476 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y4I 
_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        8R5V 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
# 
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 
Y4I O11    O1  O 0 1 N N N N N N 6.260  -0.080 18.981 -4.216 -0.184 -1.699 O11    Y4I 1  
Y4I O13    O2  O 0 1 N N N N N N 3.276  -5.246 17.475 -8.984 1.484  1.612  O13    Y4I 2  
Y4I C20    C1  C 0 1 N N N N N N 3.975  -4.330 17.923 -7.885 1.295  1.121  C20    Y4I 3  
Y4I N19    N1  N 0 1 N N N N N N 3.987  -4.095 19.298 -7.123 2.339  0.737  N19    Y4I 4  
Y4I C18    C2  C 0 1 N N N N N N 4.708  -3.121 19.960 -5.909 2.128  0.195  C18    Y4I 5  
Y4I O12    O3  O 0 1 N N N N N N 4.655  -2.984 21.181 -5.232 3.079  -0.147 O12    Y4I 6  
Y4I C21    C3  C 0 1 N N N N N N 4.811  -3.450 17.133 -7.395 -0.023 0.955  C21    Y4I 7  
Y4I C22    C4  C 0 1 N N N N N N 5.521  -2.490 17.745 -6.174 -0.205 0.408  C22    Y4I 8  
Y4I N17    N2  N 0 1 N N N N N N 5.474  -2.311 19.125 -5.433 0.881  0.026  N17    Y4I 9  
Y4I C12    C5  C 0 1 N N R N N N 6.320  -1.266 19.753 -4.108 0.684  -0.567 C12    Y4I 10 
Y4I C13    C6  C 0 1 N N N N N N 7.738  -1.848 19.834 -3.174 0.050  0.468  C13    Y4I 11 
Y4I N14    N3  N 0 1 N N N N N N 8.775  -0.834 20.009 -1.870 -0.216 -0.156 N14    Y4I 12 
Y4I C15    C7  C 0 1 N N N N N N 8.576  0.365  19.205 -2.019 -1.109 -1.314 C15    Y4I 13 
Y4I C16    C8  C 0 1 N N S N N N 7.181  0.868  19.525 -2.964 -0.464 -2.331 C16    Y4I 14 
Y4I C23    C9  C 0 1 N N N N N N 6.854  2.234  18.993 -3.186 -1.423 -3.502 C23    Y4I 15 
Y4I O15    O4  O 0 1 N N N N N N 7.517  3.184  19.837 -3.978 -0.779 -4.502 O15    Y4I 16 
Y4I P      P1  P 0 1 N N S N N N 10.193 -1.720 20.642 -0.786 -0.854 0.963  P      Y4I 17 
Y4I SP     S1  S 0 1 N N N N N N 11.544 -1.896 19.230 -1.463 -2.453 1.640  SP     Y4I 18 
Y4I OP1    O5  O 0 1 N N N N N N 9.963  -3.023 21.403 -0.579 0.193  2.167  OP1    Y4I 19 
Y4I "O5'"  O6  O 0 1 N N N N N N 10.673 -0.602 21.665 0.627  -1.132 0.243  "O5'"  Y4I 20 
Y4I "C5'"  C10 C 0 1 N N N N N N 9.862  -0.183 22.809 1.723  -1.770 0.900  "C5'"  Y4I 21 
Y4I "C4'"  C11 C 0 1 N N R N N N 10.791 0.406  23.848 2.906  -1.876 -0.065 "C4'"  Y4I 22 
Y4I "C3'"  C12 C 0 1 N N S N N N 11.870 1.388  23.361 4.107  -2.577 0.618  "C3'"  Y4I 23 
Y4I "O3'"  O7  O 0 1 N N N N N N 11.979 2.434  24.301 4.006  -3.997 0.495  "O3'"  Y4I 24 
Y4I "C2'"  C13 C 0 1 N N N N N N 13.148 0.578  23.399 5.306  -2.035 -0.198 "C2'"  Y4I 25 
Y4I "C1'"  C14 C 0 1 N N R N N N 12.908 -0.402 24.533 4.769  -0.743 -0.845 "C1'"  Y4I 26 
Y4I "O4'"  O8  O 0 1 N N N N N N 11.503 -0.669 24.552 3.419  -0.565 -0.386 "O4'"  Y4I 27 
Y4I N1     N4  N 0 1 N N N N N N 13.605 -1.741 24.356 5.592  0.398  -0.437 N1     Y4I 28 
Y4I C6     C15 C 0 1 N N N N N N 13.097 -2.681 23.517 6.322  1.076  -1.375 C6     Y4I 29 
Y4I C5     C16 C 0 1 N N N N N N 13.672 -3.886 23.346 7.081  2.128  -0.999 C5     Y4I 30 
Y4I C5M    C17 C 0 1 N N N N N N 13.138 -4.980 22.428 7.891  2.888  -2.017 C5M    Y4I 31 
Y4I C4     C18 C 0 1 N N N N N N 14.915 -4.125 24.037 7.103  2.509  0.365  C4     Y4I 32 
Y4I O4     O9  O 0 1 N N N N N N 15.547 -5.176 23.990 7.779  3.454  0.728  O4     Y4I 33 
Y4I N3     N5  N 0 1 N N N N N N 15.363 -3.156 24.891 6.370  1.814  1.258  N3     Y4I 34 
Y4I C2     C19 C 0 1 N N N N N N 14.776 -1.939 25.076 5.619  0.773  0.855  C2     Y4I 35 
Y4I O2     O10 O 0 1 N N N N N N 15.295 -1.128 25.783 4.958  0.159  1.670  O2     Y4I 36 
Y4I H1     H1  H 0 1 N N N N N N 3.416  -4.692 19.861 -7.450 3.244  0.851  H1     Y4I 37 
Y4I H2     H2  H 0 1 N N N N N N 4.862  -3.565 16.060 -7.989 -0.871 1.261  H2     Y4I 38 
Y4I H22    H3  H 0 1 N N N N N N 6.146  -1.839 17.151 -5.783 -1.202 0.273  H22    Y4I 39 
Y4I H12    H4  H 0 1 N N N N N N 5.961  -1.073 20.775 -3.704 1.645  -0.883 H12    Y4I 40 
Y4I H131   H5  H 0 0 N N N N N N 7.782  -2.541 20.687 -3.044 0.734  1.307  H131   Y4I 41 
Y4I H132   H6  H 0 0 N N N N N N 7.942  -2.398 18.904 -3.606 -0.885 0.823  H132   Y4I 42 
Y4I H151   H7  H 0 0 N N N N N N 9.325  1.127  19.467 -1.045 -1.272 -1.775 H151   Y4I 43 
Y4I H152   H8  H 0 0 N N N N N N 8.657  0.123  18.135 -2.431 -2.064 -0.987 H152   Y4I 44 
Y4I H16    H9  H 0 1 N N N N N N 7.071  0.891  20.619 -2.526 0.464  -2.698 H16    Y4I 45 
Y4I H231   H10 H 0 0 N N N N N N 5.767  2.399  19.020 -2.224 -1.706 -3.928 H231   Y4I 46 
Y4I H232   H11 H 0 0 N N N N N N 7.214  2.332  17.958 -3.704 -2.315 -3.148 H232   Y4I 47 
Y4I HO15   H12 H 0 0 N N N N N N 7.333  4.064  19.530 -4.159 -1.330 -5.276 HO15   Y4I 48 
Y4I HOP1   H13 H 0 0 N N N N N N 10.527 -3.701 21.049 -0.228 1.050  1.887  HOP1   Y4I 49 
Y4I "H5'2" H14 H 0 0 N N N N N N 9.130  0.574  22.491 2.016  -1.183 1.771  "H5'2" Y4I 50 
Y4I "H5'1" H15 H 0 0 N N N N N N 9.333  -1.051 23.230 1.424  -2.768 1.219  "H5'1" Y4I 51 
Y4I "H4'"  H16 H 0 1 N N N N N N 10.170 0.941  24.582 2.613  -2.406 -0.971 "H4'"  Y4I 52 
Y4I "H3'"  H17 H 0 1 N N N N N N 11.650 1.744  22.344 4.185  -2.283 1.665  "H3'"  Y4I 53 
Y4I "HO3'" H18 H 0 0 N N N N N N 12.643 3.050  24.014 4.735  -4.480 0.907  "HO3'" Y4I 54 
Y4I "H2'2" H19 H 0 0 N N N N N N 13.307 0.049  22.448 6.145  -1.811 0.461  "H2'2" Y4I 55 
Y4I "H2'1" H20 H 0 0 N N N N N N 14.015 1.221  23.611 5.603  -2.752 -0.962 "H2'1" Y4I 56 
Y4I "H1'"  H21 H 0 1 N N N N N N 13.228 0.053  25.482 4.781  -0.840 -1.931 "H1'"  Y4I 57 
Y4I H6     H22 H 0 1 N N N N N N 12.197 -2.453 22.966 6.293  0.771  -2.410 H6     Y4I 58 
Y4I H5M3   H23 H 0 0 N N N N N N 12.190 -4.651 21.977 7.292  3.702  -2.425 H5M3   Y4I 59 
Y4I H5M1   H24 H 0 0 N N N N N N 13.871 -5.182 21.633 8.782  3.296  -1.541 H5M1   Y4I 60 
Y4I H5M2   H25 H 0 0 N N N N N N 12.968 -5.897 23.011 8.186  2.215  -2.822 H5M2   Y4I 61 
Y4I H3     H26 H 0 1 N N N N N N 16.186 -3.355 25.422 6.380  2.069  2.194  H3     Y4I 62 
# 
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 
Y4I OP1   P      SING N N 1  
Y4I SP    P      DOUB N N 2  
Y4I "O5'" P      SING N N 3  
Y4I P     N14    SING N N 4  
Y4I "C5'" "O5'"  SING N N 5  
Y4I "C4'" "C5'"  SING N N 6  
Y4I "C4'" "O4'"  SING N N 7  
Y4I "C3'" "C4'"  SING N N 8  
Y4I "O4'" "C1'"  SING N N 9  
Y4I "O3'" "C3'"  SING N N 10 
Y4I "C2'" "C3'"  SING N N 11 
Y4I "C1'" "C2'"  SING N N 12 
Y4I N1    "C1'"  SING N N 13 
Y4I N1    C2     SING N N 14 
Y4I C6    N1     SING N N 15 
Y4I O2    C2     DOUB N N 16 
Y4I C2    N3     SING N N 17 
Y4I N3    C4     SING N N 18 
Y4I O4    C4     DOUB N N 19 
Y4I C4    C5     SING N N 20 
Y4I C5M   C5     SING N N 21 
Y4I C5    C6     DOUB N N 22 
Y4I O11   C12    SING N N 23 
Y4I O11   C16    SING N N 24 
Y4I C13   C12    SING N N 25 
Y4I C12   N17    SING N N 26 
Y4I O12   C18    DOUB N N 27 
Y4I N14   C13    SING N N 28 
Y4I C20   O13    DOUB N N 29 
Y4I C15   N14    SING N N 30 
Y4I C16   C15    SING N N 31 
Y4I O15   C23    SING N N 32 
Y4I C23   C16    SING N N 33 
Y4I N17   C18    SING N N 34 
Y4I N17   C22    SING N N 35 
Y4I C18   N19    SING N N 36 
Y4I N19   C20    SING N N 37 
Y4I C21   C20    SING N N 38 
Y4I C22   C21    DOUB N N 39 
Y4I N19   H1     SING N N 40 
Y4I C21   H2     SING N N 41 
Y4I C22   H22    SING N N 42 
Y4I C12   H12    SING N N 43 
Y4I C13   H131   SING N N 44 
Y4I C13   H132   SING N N 45 
Y4I C15   H151   SING N N 46 
Y4I C15   H152   SING N N 47 
Y4I C16   H16    SING N N 48 
Y4I C23   H231   SING N N 49 
Y4I C23   H232   SING N N 50 
Y4I O15   HO15   SING N N 51 
Y4I OP1   HOP1   SING N N 52 
Y4I "C5'" "H5'2" SING N N 53 
Y4I "C5'" "H5'1" SING N N 54 
Y4I "C4'" "H4'"  SING N N 55 
Y4I "C3'" "H3'"  SING N N 56 
Y4I "O3'" "HO3'" SING N N 57 
Y4I "C2'" "H2'2" SING N N 58 
Y4I "C2'" "H2'1" SING N N 59 
Y4I "C1'" "H1'"  SING N N 60 
Y4I C6    H6     SING N N 61 
Y4I C5M   H5M3   SING N N 62 
Y4I C5M   H5M1   SING N N 63 
Y4I C5M   H5M2   SING N N 64 
Y4I N3    H3     SING N N 65 
# 
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 
Y4I InChI            InChI                1.06  "InChI=1S/C19H26N5O10PS/c1-10-5-24(19(30)21-17(10)28)15-4-12(26)13(34-15)9-32-35(31,36)22-6-11(8-25)33-16(7-22)23-3-2-14(27)20-18(23)29/h2-3,5,11-13,15-16,25-26H,4,6-9H2,1H3,(H,31,36)(H,20,27,29)(H,21,28,30)/t11-,12-,13+,15+,16+,35-/m0/s1" 
Y4I InChIKey         InChI                1.06  JMOYBKKBBMXKAB-OTRGKRLXSA-N                                                                                                                                                                                                                     
Y4I SMILES_CANONICAL CACTVS               3.385 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@](O)(=S)N3C[C@@H](CO)O[C@H](C3)N4C=CC(=O)NC4=O)O2)C(=O)NC1=O"                                                                                                                                                
Y4I SMILES           CACTVS               3.385 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=S)N3C[CH](CO)O[CH](C3)N4C=CC(=O)NC4=O)O2)C(=O)NC1=O"                                                                                                                                                        
Y4I SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=S)(N3C[C@H](O[C@H](C3)N4C=CC(=O)NC4=O)CO)O)O"                                                                                                                                                 
Y4I SMILES           "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=S)(N3CC(OC(C3)N4C=CC(=O)NC4=O)CO)O)O"                                                                                                                                                                         
# 
_pdbx_chem_comp_identifier.comp_id           Y4I 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "1-[(2~{R},4~{S},5~{R})-5-[[[(2~{R},6~{S})-2-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-6-(hydroxymethyl)morpholin-4-yl]-oxidanyl-phosphinothioyl]oxymethyl]-4-oxidanyl-oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
Y4I "Create component" 2023-11-20 PDBE 
Y4I "Initial release"  2023-12-06 RCSB 
# 
