data_A1ACD
# 
_chem_comp.id                                    A1ACD 
_chem_comp.name                                  "1-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]-beta-D-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C11 H19 N2 O13 P3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-01-10 
_chem_comp.pdbx_modified_date                    2024-05-03 
_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                        480.195 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1ACD 
_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        8VFD 
_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 
A1ACD C01  C1  C 0 1 N N N N N N 11.806 6.877  9.634  7.234  -3.102 1.700  C01  A1ACD 1  
A1ACD C02  C2  C 0 1 N N N N N N 11.252 6.682  8.257  6.429  -2.225 0.776  C02  A1ACD 2  
A1ACD C03  C3  C 0 1 N N N N N N 9.924  6.364  8.056  5.715  -1.188 1.266  C03  A1ACD 3  
A1ACD C05  C4  C 0 1 N N R N N N 8.021  5.825  6.593  4.216  0.723  0.944  C05  A1ACD 4  
A1ACD C06  C5  C 0 1 N N N N N N 7.947  4.639  6.296  4.731  2.055  0.355  C06  A1ACD 5  
A1ACD C07  C6  C 0 1 N N R N N N 7.735  3.946  7.627  3.451  2.897  0.155  C07  A1ACD 6  
A1ACD C09  C7  C 0 1 N N R N N N 6.737  4.873  8.247  2.314  1.974  0.646  C09  A1ACD 7  
A1ACD C10  C8  C 0 1 N N N N N N 6.671  4.632  9.843  1.071  2.149  -0.228 C10  A1ACD 8  
A1ACD C15  C9  C 0 1 N N N N N N 9.188  2.571  11.388 -2.501 0.119  0.540  C15  A1ACD 9  
A1ACD C25  C10 C 0 1 N N N N N N 10.274 6.336  5.767  4.982  -0.651 -0.909 C25  A1ACD 10 
A1ACD C28  C11 C 0 1 N N N N N N 12.031 6.810  7.156  6.416  -2.473 -0.618 C28  A1ACD 11 
A1ACD N04  N1  N 0 1 N N N N N N 9.471  6.191  6.808  4.990  -0.402 0.413  N04  A1ACD 12 
A1ACD N27  N2  N 0 1 N N N N N N 11.526 6.635  5.920  5.689  -1.674 -1.425 N27  A1ACD 13 
A1ACD O08  O1  O 0 1 N N N N N N 7.247  2.661  7.496  3.507  4.089  0.942  O08  A1ACD 14 
A1ACD O11  O2  O 0 1 N N N N N N 8.041  4.971  10.323 -0.004 1.376  0.311  O11  A1ACD 15 
A1ACD O13  O3  O 0 1 N N N N N N 7.485  4.350  12.777 -1.350 0.916  -1.773 O13  A1ACD 16 
A1ACD O14  O4  O 0 1 N N N N N N 9.778  5.184  12.105 -2.148 2.781  -0.271 O14  A1ACD 17 
A1ACD O17  O5  O 0 1 N N N N N N 7.871  1.010  9.517  -4.042 -0.348 -1.633 O17  A1ACD 18 
A1ACD O18  O6  O 0 1 N N N N N N 6.473  1.778  11.487 -4.839 1.517  -0.131 O18  A1ACD 19 
A1ACD O19  O7  O 0 1 N N N N N N 8.304  -0.044 11.872 -5.072 -1.005 0.575  O19  A1ACD 20 
A1ACD O21  O8  O 0 1 N N N N N N 7.327  -0.916 13.973 -7.464 -0.363 0.087  O21  A1ACD 21 
A1ACD O22  O9  O 0 1 N N N N N N 8.109  1.316  13.925 -6.671 -2.601 -0.770 O22  A1ACD 22 
A1ACD O23  O10 O 0 1 N N N N N N 9.752  -0.445 13.920 -7.082 -2.184 1.793  O23  A1ACD 23 
A1ACD O24  O11 O 0 1 N N N N N N 7.213  5.987  7.991  2.841  0.636  0.511  O24  A1ACD 24 
A1ACD O26  O12 O 0 1 N N N N N N 9.900  6.195  4.697  4.331  0.060  -1.650 O26  A1ACD 25 
A1ACD O29  O13 O 0 1 N N N N N N 13.215 7.078  7.283  7.056  -3.398 -1.083 O29  A1ACD 26 
A1ACD P12  P1  P 0 1 N N N N N N 8.599  4.307  11.691 -1.468 1.324  -0.356 P12  A1ACD 27 
A1ACD P16  P2  P 0 1 N N N N N N 7.897  1.289  11.012 -4.159 0.060  -0.216 P16  A1ACD 28 
A1ACD P20  P3  P 0 1 N N N N N N 8.360  -0.019 13.429 -6.591 -1.513 0.414  P20  A1ACD 29 
A1ACD H011 H1  H 0 0 N N N N N N 12.876 7.122  9.568  7.739  -3.874 1.120  H011 A1ACD 30 
A1ACD H013 H2  H 0 0 N N N N N N 11.271 7.700  10.131 7.974  -2.497 2.223  H013 A1ACD 31 
A1ACD H012 H3  H 0 0 N N N N N N 11.677 5.952  10.215 6.569  -3.570 2.427  H012 A1ACD 32 
A1ACD H031 H4  H 0 0 N N N N N N 9.256  6.256  8.898  5.717  -0.981 2.326  H031 A1ACD 33 
A1ACD H051 H5  H 0 0 N N N N N N 7.573  6.508  5.856  4.271  0.740  2.032  H051 A1ACD 34 
A1ACD H062 H6  H 0 0 N N N N N N 7.099  4.457  5.620  5.406  2.547  1.056  H062 A1ACD 35 
A1ACD H061 H7  H 0 0 N N N N N N 8.877  4.296  5.819  5.231  1.884  -0.598 H061 A1ACD 36 
A1ACD H071 H8  H 0 0 N N N N N N 8.671  3.966  8.205  3.316  3.142  -0.898 H071 A1ACD 37 
A1ACD H091 H9  H 0 0 N N N N N N 5.738  4.693  7.823  2.077  2.185  1.689  H091 A1ACD 38 
A1ACD H102 H10 H 0 0 N N N N N N 6.427  3.583  10.069 0.786  3.201  -0.248 H102 A1ACD 39 
A1ACD H101 H11 H 0 0 N N N N N N 5.922  5.291  10.306 1.288  1.812  -1.241 H101 A1ACD 40 
A1ACD H152 H12 H 0 0 N N N N N N 9.882  2.601  10.535 -2.041 -0.868 0.482  H152 A1ACD 41 
A1ACD H151 H13 H 0 0 N N N N N N 9.728  2.243  12.289 -2.588 0.419  1.584  H151 A1ACD 42 
A1ACD H271 H14 H 0 0 N N N N N N 12.117 6.736  5.120  5.675  -1.838 -2.381 H271 A1ACD 43 
A1ACD H081 H15 H 0 0 N N N N N N 7.510  2.144  8.248  4.240  4.676  0.714  H081 A1ACD 44 
A1ACD H1   H16 H 0 1 N N N N N N 9.596  5.583  12.948 -2.257 3.113  0.631  H1   A1ACD 45 
A1ACD H2   H17 H 0 1 N N N N N N 5.881  1.801  10.744 -4.948 1.849  0.771  H2   A1ACD 46 
A1ACD H3   H18 H 0 1 N N N N N N 7.341  1.307  14.484 -6.122 -3.384 -0.622 H3   A1ACD 47 
A1ACD H4   H19 H 0 1 N N N N N N 9.671  -1.207 14.481 -7.990 -2.513 1.769  H4   A1ACD 48 
# 
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 
A1ACD C02 C01  SING N N 1  
A1ACD C03 C02  DOUB N N 2  
A1ACD N04 C03  SING N N 3  
A1ACD C06 C05  SING N N 4  
A1ACD C07 C06  SING N N 5  
A1ACD O08 C07  SING N N 6  
A1ACD C09 C07  SING N N 7  
A1ACD O11 C10  SING N N 8  
A1ACD P12 O11  SING N N 9  
A1ACD O13 P12  DOUB N N 10 
A1ACD O14 P12  SING N N 11 
A1ACD C15 P12  SING N N 12 
A1ACD P16 C15  SING N N 13 
A1ACD O17 P16  DOUB N N 14 
A1ACD O18 P16  SING N N 15 
A1ACD O19 P16  SING N N 16 
A1ACD P20 O19  SING N N 17 
A1ACD O21 P20  DOUB N N 18 
A1ACD O22 P20  SING N N 19 
A1ACD O23 P20  SING N N 20 
A1ACD C10 C09  SING N N 21 
A1ACD O24 C09  SING N N 22 
A1ACD C05 N04  SING N N 23 
A1ACD C25 N04  SING N N 24 
A1ACD O26 C25  DOUB N N 25 
A1ACD N27 C25  SING N N 26 
A1ACD C28 N27  SING N N 27 
A1ACD O29 C28  DOUB N N 28 
A1ACD C02 C28  SING N N 29 
A1ACD C05 O24  SING N N 30 
A1ACD C01 H011 SING N N 31 
A1ACD C01 H013 SING N N 32 
A1ACD C01 H012 SING N N 33 
A1ACD C03 H031 SING N N 34 
A1ACD C05 H051 SING N N 35 
A1ACD C06 H062 SING N N 36 
A1ACD C06 H061 SING N N 37 
A1ACD C07 H071 SING N N 38 
A1ACD C09 H091 SING N N 39 
A1ACD C10 H102 SING N N 40 
A1ACD C10 H101 SING N N 41 
A1ACD C15 H152 SING N N 42 
A1ACD C15 H151 SING N N 43 
A1ACD N27 H271 SING N N 44 
A1ACD O08 H081 SING N N 45 
A1ACD O14 H1   SING N N 46 
A1ACD O18 H2   SING N N 47 
A1ACD O22 H3   SING N N 48 
A1ACD O23 H4   SING N N 49 
# 
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 
A1ACD SMILES           ACDLabs              12.01 "O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC1OC(CC1O)N1C=C(C)C(=O)NC1=O"                                                                                                                                    
A1ACD InChI            InChI                1.06  "InChI=1S/C11H19N2O13P3/c1-6-3-13(11(16)12-10(6)15)9-2-7(14)8(25-9)4-24-27(17,18)5-28(19,20)26-29(21,22)23/h3,7-9,14H,2,4-5H2,1H3,(H,17,18)(H,19,20)(H,12,15,16)(H2,21,22,23)/t7-,8-,9-/m1/s1" 
A1ACD InChIKey         InChI                1.06  AFUOLHFRDGMFSB-IWSPIJDZSA-N                                                                                                                                                                    
A1ACD SMILES_CANONICAL CACTVS               3.385 "CC1=CN([C@H]2C[C@@H](O)[C@@H](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                              
A1ACD SMILES           CACTVS               3.385 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                                   
A1ACD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O"                                                                                                                     
A1ACD SMILES           "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(CP(=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 
A1ACD "SYSTEMATIC NAME" ACDLabs              12.01 "1-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]-beta-D-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione"            
A1ACD "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-[[oxidanyl(phosphonooxy)phosphoryl]methyl]phosphinic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1ACD "Create component" 2024-01-10 RCSB 
A1ACD "Initial release"  2024-05-08 RCSB 
# 
