data_YWQ
# 
_chem_comp.id                                    YWQ 
_chem_comp.name                                  
;uridine 5'-heptaphosphate
;
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C9 H19 N2 O27 P7" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-03-02 
_chem_comp.pdbx_modified_date                    2024-03-01 
_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                        804.061 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YWQ 
_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        8GC9 
_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_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 
YWQ C10 C1  C 0 1 N N N N N N -37.179 1.320  10.716 5.861  5.281  -0.094 C10 YWQ 1  
YWQ C15 C2  C 0 1 N N S N N N -36.998 -3.381 10.615 6.208  0.904  1.613  C15 YWQ 2  
YWQ C02 C3  C 0 1 N N S N N N -38.418 -2.909 11.150 7.616  1.539  1.625  C02 YWQ 3  
YWQ C03 C4  C 0 1 N N R N N N -38.350 -1.350 11.170 7.370  3.005  1.204  C03 YWQ 4  
YWQ C04 C5  C 0 1 N N S N N N -37.301 -1.141 10.063 5.843  3.083  0.988  C04 YWQ 5  
YWQ C06 C6  C 0 1 N N N N N N -35.353 0.344  9.446  4.925  3.441  -1.234 C06 YWQ 6  
YWQ C08 C7  C 0 1 N N N N N N -35.305 2.737  10.134 4.930  5.533  -2.275 C08 YWQ 7  
YWQ C09 C8  C 0 1 N N N N N N -36.575 2.544  10.761 5.574  6.084  -1.141 C09 YWQ 8  
YWQ C16 C9  C 0 1 N N N N N N -36.078 -4.123 11.667 6.277  -0.536 1.100  C16 YWQ 9  
YWQ N05 N1  N 0 1 N N N N N N -36.605 0.230  10.094 5.532  3.954  -0.148 N05 YWQ 10 
YWQ N07 N2  N 0 1 N N N N N N -34.744 1.617  9.498  4.627  4.219  -2.291 N07 YWQ 11 
YWQ O01 O1  O 0 1 N N N N N N -38.651 -3.209 12.467 8.469  0.884  0.683  O01 YWQ 12 
YWQ O11 O2  O 0 1 N N N N N N -34.643 3.799  10.098 4.661  6.237  -3.231 O11 YWQ 13 
YWQ O12 O3  O 0 1 N N N N N N -34.760 -0.561 8.858  4.646  2.259  -1.262 O12 YWQ 14 
YWQ O13 O4  O 0 1 N N N N N N -36.375 -2.153 10.169 5.441  1.725  0.706  O13 YWQ 15 
YWQ O14 O5  O 0 1 N N N N N N -37.887 -0.880 12.384 8.063  3.301  -0.010 O14 YWQ 16 
YWQ O17 O6  O 0 1 N N N N N N -36.037 -5.448 11.455 4.987  -1.142 1.206  O17 YWQ 17 
YWQ O19 O7  O 0 1 N N N N N N -36.574 -7.878 12.152 5.110  -2.846 -0.652 O19 YWQ 18 
YWQ O20 O8  O 0 1 N N N N N N -38.480 -6.585 10.884 3.116  -2.962 0.892  O20 YWQ 19 
YWQ O22 O9  O 0 1 N N N N N N -40.977 -7.333 10.487 2.294  -5.431 1.269  O22 YWQ 20 
YWQ O23 O10 O 0 1 N N N N N N -40.655 -5.089 11.769 0.623  -3.611 0.368  O23 YWQ 21 
YWQ O25 O11 O 0 1 N N N N N N -41.629 -6.515 13.561 -0.473 -4.583 -1.687 O25 YWQ 22 
YWQ O26 O12 O 0 1 N N N N N N -42.170 -3.966 13.694 -1.818 -2.931 -0.333 O26 YWQ 23 
YWQ O28 O13 O 0 1 N N N N N N -43.751 -1.910 13.886 -2.904 -2.336 -2.652 O28 YWQ 24 
YWQ O29 O14 O 0 1 N N N N N N -42.676 -2.229 11.606 -4.002 -1.470 -0.426 O29 YWQ 25 
YWQ O31 O15 O 0 1 N N N N N N -42.901 -2.969 9.305  -6.108 -1.167 -1.784 O31 YWQ 26 
YWQ O32 O16 O 0 1 N N N N N N -44.947 -1.563 10.077 -5.626 0.553  -0.000 O32 YWQ 27 
YWQ O34 O17 O 0 1 N N N N N N -46.681 0.517  9.782  -6.388 2.921  0.851  O34 YWQ 28 
YWQ O35 O18 O 0 1 N N N N N N -45.557 0.001  12.006 -6.901 2.185  -1.620 O35 YWQ 29 
YWQ O36 O19 O 0 1 N N N N N N -44.205 0.960  10.031 -8.065 1.105  0.342  O36 YWQ 30 
YWQ O37 O20 O 0 1 N N N N N N -44.612 -3.842 11.079 -6.378 -1.889 0.619  O37 YWQ 31 
YWQ O38 O21 O 0 1 N N N N N N -41.206 -1.641 13.636 -4.030 -3.918 -1.040 O38 YWQ 32 
YWQ O39 O22 O 0 1 N N N N N N -39.869 -4.812 14.237 -1.334 -5.357 0.556  O39 YWQ 33 
YWQ O40 O23 O 0 1 N N N N N N -39.851 -5.293 9.432  2.529  -4.463 -1.051 O40 YWQ 34 
YWQ O41 O24 O 0 1 N N N N N N -37.783 -6.042 13.321 5.516  -3.670 1.699  O41 YWQ 35 
YWQ O43 O25 O 0 1 N N N N N N -48.839 0.139  11.404 -7.587 5.214  0.386  O43 YWQ 36 
YWQ O44 O26 O 0 1 N N N N N N -49.127 0.439  8.943  -8.477 3.589  2.101  O44 YWQ 37 
YWQ O45 O27 O 0 1 N N N N N N -48.445 2.403  10.421 -6.347 4.818  2.670  O45 YWQ 38 
YWQ P18 P1  P 0 1 N N N N N N -37.399 -6.631 11.988 4.692  -2.659 0.755  P18 YWQ 39 
YWQ P21 P2  P 0 1 N N N N N N -40.204 -6.062 10.658 2.149  -4.124 0.339  P21 YWQ 40 
YWQ P24 P3  P 0 1 N N N N N N -41.121 -5.101 13.454 -0.744 -4.130 -0.304 P24 YWQ 41 
YWQ P27 P4  P 0 1 N N N N N N -42.479 -2.294 13.165 -3.207 -2.691 -1.111 P27 YWQ 42 
YWQ P30 P5  P 0 1 N N N N N N -43.885 -2.706 10.426 -5.541 -0.997 -0.428 P30 YWQ 43 
YWQ P33 P6  P 0 1 N N N N N N -45.326 0.080  10.517 -6.773 1.678  -0.097 P33 YWQ 44 
YWQ P42 P7  P 0 1 N N N N N N -48.345 0.905  10.168 -7.227 4.124  1.515  P42 YWQ 45 
YWQ H1  H1  H 0 1 N N N N N N -38.144 1.200  11.186 6.353  5.683  0.779  H1  YWQ 46 
YWQ H2  H2  H 0 1 N N N N N N -37.159 -4.055 9.761  5.772  0.929  2.612  H2  YWQ 47 
YWQ H3  H3  H 0 1 N N N N N N -39.213 -3.253 10.472 8.046  1.495  2.625  H3  YWQ 48 
YWQ H4  H4  H 0 1 N N N N N N -39.318 -0.918 10.877 7.681  3.687  1.996  H4  YWQ 49 
YWQ H5  H5  H 0 1 N N N N N N -37.823 -1.222 9.098  5.348  3.445  1.890  H5  YWQ 50 
YWQ H6  H6  H 0 1 N N N N N N -37.057 3.366  11.270 5.833  7.132  -1.114 H6  YWQ 51 
YWQ H7  H7  H 0 1 N N N N N N -35.057 -3.720 11.592 6.593  -0.535 0.057  H7  YWQ 52 
YWQ H8  H8  H 0 1 N N N N N N -36.473 -3.937 12.677 6.994  -1.100 1.696  H8  YWQ 53 
YWQ H9  H9  H 0 1 N N N N N N -33.855 1.729  9.053  4.189  3.834  -3.066 H9  YWQ 54 
YWQ H10 H10 H 0 1 N N N N N N -39.514 -2.899 12.715 9.366  1.243  0.649  H10 YWQ 55 
YWQ H11 H11 H 0 1 N N N N N N -38.549 -1.019 13.051 9.024  3.208  0.053  H11 YWQ 56 
YWQ H12 H12 H 0 1 N N N N N N -41.145 -7.480 9.564  2.060  -5.282 2.195  H12 YWQ 57 
YWQ H13 H13 H 0 1 N N N N N N -43.551 -1.279 14.567 -2.367 -1.541 -2.775 H13 YWQ 58 
YWQ H14 H14 H 0 1 N N N N N N -44.925 0.550  12.455 -6.089 2.573  -1.975 H14 YWQ 59 
YWQ H15 H15 H 0 1 N N N N N N -44.346 -4.661 10.678 -6.061 -1.827 1.531  H15 YWQ 60 
YWQ H16 H16 H 0 1 N N N N N N -39.590 -5.599 14.690 -1.535 -5.133 1.474  H16 YWQ 61 
YWQ H17 H17 H 0 1 N N N N N N -37.426 -6.578 14.019 5.293  -3.602 2.637  H17 YWQ 62 
YWQ H18 H18 H 0 1 N N N N N N -49.527 -0.464 11.149 -6.814 5.607  -0.041 H18 YWQ 63 
YWQ H19 H19 H 0 1 N N N N N N -48.992 2.801  9.754  -6.791 5.553  3.115  H19 YWQ 64 
# 
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 
YWQ O12 C06 DOUB N N 1  
YWQ O44 P42 DOUB N N 2  
YWQ O31 P30 DOUB N N 3  
YWQ O40 P21 DOUB N N 4  
YWQ C06 N07 SING N N 5  
YWQ C06 N05 SING N N 6  
YWQ N07 C08 SING N N 7  
YWQ O34 P42 SING N N 8  
YWQ O34 P33 SING N N 9  
YWQ O36 P33 DOUB N N 10 
YWQ C04 N05 SING N N 11 
YWQ C04 O13 SING N N 12 
YWQ C04 C03 SING N N 13 
YWQ O32 P30 SING N N 14 
YWQ O32 P33 SING N N 15 
YWQ N05 C10 SING N N 16 
YWQ O11 C08 DOUB N N 17 
YWQ C08 C09 SING N N 18 
YWQ P42 O45 SING N N 19 
YWQ P42 O43 SING N N 20 
YWQ O13 C15 SING N N 21 
YWQ P30 O37 SING N N 22 
YWQ P30 O29 SING N N 23 
YWQ O22 P21 SING N N 24 
YWQ P33 O35 SING N N 25 
YWQ C15 C02 SING N N 26 
YWQ C15 C16 SING N N 27 
YWQ P21 O20 SING N N 28 
YWQ P21 O23 SING N N 29 
YWQ C10 C09 DOUB N N 30 
YWQ O20 P18 SING N N 31 
YWQ C02 C03 SING N N 32 
YWQ C02 O01 SING N N 33 
YWQ C03 O14 SING N N 34 
YWQ O17 C16 SING N N 35 
YWQ O17 P18 SING N N 36 
YWQ O29 P27 SING N N 37 
YWQ O23 P24 SING N N 38 
YWQ P18 O19 DOUB N N 39 
YWQ P18 O41 SING N N 40 
YWQ P27 O38 DOUB N N 41 
YWQ P27 O26 SING N N 42 
YWQ P27 O28 SING N N 43 
YWQ P24 O25 DOUB N N 44 
YWQ P24 O26 SING N N 45 
YWQ P24 O39 SING N N 46 
YWQ C10 H1  SING N N 47 
YWQ C15 H2  SING N N 48 
YWQ C02 H3  SING N N 49 
YWQ C03 H4  SING N N 50 
YWQ C04 H5  SING N N 51 
YWQ C09 H6  SING N N 52 
YWQ C16 H7  SING N N 53 
YWQ C16 H8  SING N N 54 
YWQ N07 H9  SING N N 55 
YWQ O01 H10 SING N N 56 
YWQ O14 H11 SING N N 57 
YWQ O22 H12 SING N N 58 
YWQ O28 H13 SING N N 59 
YWQ O35 H14 SING N N 60 
YWQ O37 H15 SING N N 61 
YWQ O39 H16 SING N N 62 
YWQ O41 H17 SING N N 63 
YWQ O43 H18 SING N N 64 
YWQ O45 H19 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 
YWQ SMILES           ACDLabs              12.01 "O=P(O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OCC1OC(N2C=CC(=O)NC2=O)C(O)C1O"                                                                                                                                                                                     
YWQ InChI            InChI                1.06  "InChI=1S/C9H19N2O27P7/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(32-8)3-31-40(19,20)34-42(23,24)36-44(27,28)38-45(29,30)37-43(25,26)35-41(21,22)33-39(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H,23,24)(H,25,26)(H,27,28)(H,29,30)(H,10,12,15)(H2,16,17,18)/t4-,6+,7+,8-/m0/s1" 
YWQ InChIKey         InChI                1.06  DLYGIJYUJNEFKD-IHBLQFBFSA-N                                                                                                                                                                                                                                                         
YWQ SMILES_CANONICAL CACTVS               3.385 "O[C@H]1[C@@H](O)[C@H](O[C@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O"                                                                                                                                                      
YWQ SMILES           CACTVS               3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O"                                                                                                                                                           
YWQ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)[C@@H]2[C@@H]([C@@H]([C@@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O"                                                                                                                                                             
YWQ SMILES           "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=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 
YWQ "SYSTEMATIC NAME" ACDLabs              12.01 "1-{5-O-[(R)-hydroxy{[(R)-hydroxy{[(R)-hydroxy{[(R)-hydroxy{[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]oxy}phosphoryl]oxy}phosphoryl]oxy}phosphoryl]-beta-L-lyxofuranosyl}pyrimidine-2,4(1H,3H)-dione"                       
YWQ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[[(2~{S},3~{S},4~{R},5~{S})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl] 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 
YWQ "Create component" 2023-03-02 RCSB 
YWQ "Initial release"  2024-03-06 RCSB 
# 
