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 #