data_A1A0L # _chem_comp.id A1A0L _chem_comp.name "1-{(2R,3R,4S)-3-hydroxy-4-[(trihydroxy-lambda~5~-phosphanyl)oxy]oxolan-2-yl}-4-methoxy-5-methylpyrimidin-2(1H)-one" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2024-07-30 _chem_comp.pdbx_modified_date 2024-09-13 _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 322.208 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1A0L _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 9CIH _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 A1A0L P P1 P 0 1 N N N N N N -62.615 -9.655 -3.544 -4.035 0.673 0.198 P A1A0L 1 A1A0L OP1 O1 O 0 1 N N N N N N -62.605 -11.169 -3.286 -5.009 -0.212 -0.478 OP1 A1A0L 2 A1A0L OP2 O2 O 0 1 N N N N N N -64.008 -9.074 -3.827 -4.137 0.465 1.791 OP2 A1A0L 3 A1A0L N1 N1 N 0 1 N N N N N N -59.224 -6.164 -2.528 1.645 -0.770 -0.232 N1 A1A0L 4 A1A0L C6 C1 C 0 1 N N N N N N -60.438 -5.711 -2.797 2.767 -1.455 0.120 C6 A1A0L 5 A1A0L C2 C2 C 0 1 N N N N N N -58.157 -5.372 -2.580 1.692 0.564 -0.410 C2 A1A0L 6 A1A0L O2 O3 O 0 1 N N N N N N -57.130 -5.823 -2.344 0.678 1.162 -0.730 O2 A1A0L 7 A1A0L N3 N2 N 0 1 N N N N N N -58.291 -4.081 -2.898 2.828 1.240 -0.243 N3 A1A0L 8 A1A0L C4 C3 C 0 1 N N N N N N -59.466 -3.530 -3.172 3.943 0.615 0.104 C4 A1A0L 9 A1A0L O4 O4 O 0 1 N N N N N N -59.573 -2.345 -3.466 5.088 1.312 0.270 O4 A1A0L 10 A1A0L C5 C4 C 0 1 N N N N N N -60.592 -4.361 -3.119 3.929 -0.780 0.293 C5 A1A0L 11 A1A0L "C4'" C5 C 0 1 N N N N N N -59.596 -9.657 -2.885 -1.581 -1.508 -1.613 "C4'" A1A0L 12 A1A0L "O4'" O5 O 0 1 N N N N N N -59.038 -8.278 -3.308 -0.177 -1.185 -1.719 "O4'" A1A0L 13 A1A0L "C3'" C6 C 0 1 N N S N N N -60.630 -9.235 -1.734 -1.997 -1.005 -0.213 "C3'" A1A0L 14 A1A0L "O3'" O6 O 0 1 N N N N N N -61.836 -8.742 -2.366 -2.546 0.311 -0.297 "O3'" A1A0L 15 A1A0L "C2'" C7 C 0 1 N N R N N N -60.080 -8.248 -1.134 -0.676 -0.991 0.588 "C2'" A1A0L 16 A1A0L "O2'" O7 O 0 1 N N N N N N -59.286 -8.717 -0.039 -0.758 -1.880 1.704 "O2'" A1A0L 17 A1A0L "C1'" C8 C 0 1 N N R N N N -59.003 -7.545 -2.212 0.382 -1.487 -0.422 "C1'" A1A0L 18 A1A0L C1 C9 C 0 1 N N N N N N -58.458 -1.446 -3.529 5.025 2.724 0.060 C1 A1A0L 19 A1A0L C3 C10 C 0 1 N N N N N N -61.994 -3.820 -3.430 5.187 -1.510 0.688 C3 A1A0L 20 A1A0L H2 H2 H 0 1 N N N N N N -64.654 -9.770 -3.795 -3.525 1.016 2.300 H2 A1A0L 21 A1A0L H3 H3 H 0 1 N N N N N N -61.292 -6.372 -2.768 2.732 -2.526 0.260 H3 A1A0L 22 A1A0L H4 H4 H 0 1 N N N N N N -60.106 -10.159 -3.720 -2.149 -0.990 -2.387 H4 A1A0L 23 A1A0L H5 H5 H 0 1 N N N N N N -58.802 -10.310 -2.494 -1.731 -2.585 -1.690 H5 A1A0L 24 A1A0L H6 H6 H 0 1 N N N N N N -60.836 -10.104 -1.092 -2.713 -1.690 0.241 H6 A1A0L 25 A1A0L H7 H7 H 0 1 N N N N N N -60.789 -7.473 -0.808 -0.443 0.020 0.923 H7 A1A0L 26 A1A0L H8 H8 H 0 1 N Y N N N N -59.848 -9.128 0.607 -1.448 -1.650 2.341 H8 A1A0L 27 A1A0L H9 H9 H 0 1 N N N N N N -58.015 -7.633 -1.737 0.536 -2.560 -0.317 H9 A1A0L 28 A1A0L H10 H10 H 0 1 N N N N N N -58.810 -0.443 -3.813 4.705 2.926 -0.962 H10 A1A0L 29 A1A0L H11 H11 H 0 1 N N N N N N -57.970 -1.398 -2.544 4.311 3.163 0.757 H11 A1A0L 30 A1A0L H12 H12 H 0 1 N N N N N N -57.738 -1.807 -4.278 6.010 3.161 0.226 H12 A1A0L 31 A1A0L H13 H13 H 0 1 N N N N N N -62.731 -4.631 -3.331 6.007 -0.797 0.782 H13 A1A0L 32 A1A0L H14 H14 H 0 1 N N N N N N -62.240 -3.013 -2.724 5.031 -2.011 1.643 H14 A1A0L 33 A1A0L H15 H15 H 0 1 N N N N N N -62.016 -3.428 -4.457 5.433 -2.249 -0.075 H15 A1A0L 34 A1A0L OP3 OP3 O 0 1 N Y N N N N -62.241 -9.423 -5.080 -4.363 2.207 -0.165 OP3 A1A0L 35 A1A0L HOP3 HOP3 H 0 0 N Y N N N N -62.094 -10.262 -5.501 -5.246 2.495 0.105 HOP3 A1A0L 36 # 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 A1A0L OP2 P SING N N 1 A1A0L P OP1 DOUB N N 2 A1A0L P "O3'" SING N N 3 A1A0L C1 O4 SING N N 4 A1A0L O4 C4 SING N N 5 A1A0L C3 C5 SING N N 6 A1A0L "O4'" "C4'" SING N N 7 A1A0L "O4'" "C1'" SING N N 8 A1A0L C4 C5 SING N N 9 A1A0L C4 N3 DOUB N N 10 A1A0L C5 C6 DOUB N N 11 A1A0L N3 C2 SING N N 12 A1A0L "C4'" "C3'" SING N N 13 A1A0L C6 N1 SING N N 14 A1A0L C2 N1 SING N N 15 A1A0L C2 O2 DOUB N N 16 A1A0L N1 "C1'" SING N N 17 A1A0L "O3'" "C3'" SING N N 18 A1A0L "C1'" "C2'" SING N N 19 A1A0L "C3'" "C2'" SING N N 20 A1A0L "C2'" "O2'" SING N N 21 A1A0L OP2 H2 SING N N 22 A1A0L C6 H3 SING N N 23 A1A0L "C4'" H4 SING N N 24 A1A0L "C4'" H5 SING N N 25 A1A0L "C3'" H6 SING N N 26 A1A0L "C2'" H7 SING N N 27 A1A0L "O2'" H8 SING N N 28 A1A0L "C1'" H9 SING N N 29 A1A0L C1 H10 SING N N 30 A1A0L C1 H11 SING N N 31 A1A0L C1 H12 SING N N 32 A1A0L C3 H13 SING N N 33 A1A0L C3 H14 SING N N 34 A1A0L C3 H15 SING N N 35 A1A0L P OP3 SING N N 36 A1A0L OP3 HOP3 SING N N 37 # 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 A1A0L SMILES ACDLabs 12.01 "O=P(O)(O)OC1COC(N2C=C(C)C(=NC2=O)OC)C1O" A1A0L InChI InChI 1.06 "InChI=1S/C10H15N2O8P/c1-5-3-12(10(14)11-8(5)18-2)9-7(13)6(4-19-9)20-21(15,16)17/h3,6-7,9,13H,4H2,1-2H3,(H2,15,16,17)/t6-,7+,9+/m0/s1" A1A0L InChIKey InChI 1.06 OJDLFCPBILBUDP-LKEWCRSYSA-N A1A0L SMILES_CANONICAL CACTVS 3.385 "COC1=NC(=O)N(C=C1C)[C@@H]2OC[C@H](O[P](O)(O)=O)[C@H]2O" A1A0L SMILES CACTVS 3.385 "COC1=NC(=O)N(C=C1C)[CH]2OC[CH](O[P](O)(O)=O)[CH]2O" A1A0L SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)N=C1OC)[C@H]2[C@@H]([C@H](CO2)OP(=O)(O)O)O" A1A0L SMILES "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)N=C1OC)C2C(C(CO2)OP(=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 A1A0L "SYSTEMATIC NAME" ACDLabs 12.01 "(3S,4R,5R)-4-hydroxy-5-(4-methoxy-5-methyl-2-oxopyrimidin-1(2H)-yl)oxolan-3-yl dihydrogen phosphate" A1A0L "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(3~{S},4~{R},5~{R})-5-(4-methoxy-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-4-oxidanyl-oxolan-3-yl] dihydrogen 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 A1A0L "Create component" 2024-07-30 RCSB A1A0L "Initial release" 2024-09-18 RCSB #