data_A1L3P # _chem_comp.id A1L3P _chem_comp.name 5-Carboxymethylaminomethyluridine _chem_comp.type non-polymer _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H18 N3 O11 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "2-[[1-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]-2,4-bis(oxidanylidene)pyrimidin-5-yl]methylamino]ethanoic acid" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2024-08-16 _chem_comp.pdbx_modified_date 2025-07-18 _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 411.259 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1L3P _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 9J5P _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ _chem_comp.pdbx_pcm ? # 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 A1L3P P P1 P 0 1 N N N N N N -53.236 12.521 -36.069 5.102 2.100 -0.115 P A1L3P 1 A1L3P O4 O1 O 0 1 N N N N N N -46.249 10.000 -39.471 -3.874 -0.864 -2.560 O4 A1L3P 2 A1L3P O6 O2 O 0 1 N N N N N N -49.615 13.471 -41.147 -5.730 3.059 0.523 O6 A1L3P 3 A1L3P "C4'" C1 C 0 1 N N R N N N -50.541 11.334 -33.640 2.638 -0.840 0.891 "C4'" A1L3P 4 A1L3P "C5'" C2 C 0 1 N N N N N N -51.211 12.456 -34.395 3.840 -0.239 0.160 "C5'" A1L3P 5 A1L3P C1 C3 C 0 1 N N N N N N -49.850 13.520 -39.911 -6.528 2.236 0.906 C1 A1L3P 6 A1L3P "C1'" C4 C 0 1 N N R N N N -48.539 10.391 -34.425 0.393 -1.288 0.722 "C1'" A1L3P 7 A1L3P C2 C5 C 0 1 N N N N N N -47.761 9.154 -36.329 -0.615 -1.186 -1.488 C2 A1L3P 8 A1L3P "C2'" C6 C 0 1 N N R N N N -48.198 11.652 -33.635 1.065 -2.668 0.546 "C2'" A1L3P 9 A1L3P C3 C7 C 0 1 N N N N N N -46.542 12.623 -38.380 -4.485 -0.819 0.177 C3 A1L3P 10 A1L3P "C3'" C8 C 0 1 N N S N N N -49.407 11.756 -32.717 2.576 -2.366 0.660 "C3'" A1L3P 11 A1L3P C4 C9 C 0 1 N N N N N N -46.823 10.119 -38.198 -2.918 -0.960 -1.813 C4 A1L3P 12 A1L3P C5 C10 C 0 1 N N N N N N -46.985 11.369 -37.622 -3.103 -0.950 -0.410 C5 A1L3P 13 A1L3P C6 C11 C 0 1 N N N N N N -47.554 11.445 -36.355 -2.026 -1.063 0.396 C6 A1L3P 14 A1L3P C7 C12 C 0 1 N N N N N N -48.836 12.968 -38.916 -6.192 0.769 0.832 C7 A1L3P 15 A1L3P N1 N1 N 0 1 N N N N N N -47.925 10.329 -35.757 -0.778 -1.176 -0.153 N1 A1L3P 16 A1L3P N2 N2 N 0 1 N N N N N N -47.483 12.933 -39.448 -4.848 0.602 0.264 N2 A1L3P 17 A1L3P N3 N3 N 0 1 N N N N N N -47.220 9.050 -37.528 -1.672 -1.079 -2.315 N3 A1L3P 18 A1L3P O1 O3 O 0 1 N N N N N N -50.925 14.019 -39.484 -7.714 2.629 1.396 O1 A1L3P 19 A1L3P O2 O4 O 0 1 N N N N N N -48.170 8.003 -35.643 0.503 -1.287 -1.955 O2 A1L3P 20 A1L3P "O2'" O5 O 0 1 N N N N N N -46.955 11.540 -32.970 0.653 -3.561 1.583 "O2'" A1L3P 21 A1L3P "O3'" O6 O 0 1 N N N N N N -49.283 10.791 -31.674 3.144 -3.064 1.770 "O3'" A1L3P 22 A1L3P "O4'" O7 O 0 1 N N N N N N -49.947 10.413 -34.595 1.405 -0.333 0.336 "O4'" A1L3P 23 A1L3P "O5'" O8 O 0 1 N N N N N N -52.581 12.168 -34.660 3.947 1.150 0.479 "O5'" A1L3P 24 A1L3P OP1 O9 O 0 1 N N N N N N -54.618 11.914 -36.110 6.427 1.515 0.187 OP1 A1L3P 25 A1L3P OP2 O10 O 0 1 N N N N N N -53.067 14.001 -36.317 4.923 2.228 -1.710 OP2 A1L3P 26 A1L3P H1 H1 H 0 1 N N N N N N -51.300 10.806 -33.044 2.694 -0.619 1.957 H1 A1L3P 27 A1L3P H2 H2 H 0 1 N N N N N N -50.687 12.606 -35.350 4.749 -0.754 0.471 H2 A1L3P 28 A1L3P H3 H3 H 0 1 N N N N N N -51.150 13.376 -33.795 3.707 -0.355 -0.916 H3 A1L3P 29 A1L3P H4 H4 H 0 1 N N N N N N -48.238 9.511 -33.838 0.104 -1.136 1.762 H4 A1L3P 30 A1L3P H5 H5 H 0 1 N N N N N N -48.193 12.513 -34.320 0.829 -3.086 -0.433 H5 A1L3P 31 A1L3P H6 H6 H 0 1 N N N N N N -45.546 12.451 -38.814 -5.201 -1.338 -0.460 H6 A1L3P 32 A1L3P H7 H7 H 0 1 N N N N N N -46.496 13.471 -37.681 -4.500 -1.259 1.174 H7 A1L3P 33 A1L3P H8 H8 H 0 1 N N N N N N -49.547 12.781 -32.344 3.089 -2.634 -0.264 H8 A1L3P 34 A1L3P H9 H9 H 0 1 N N N N N N -47.690 12.400 -35.870 -2.148 -1.061 1.469 H9 A1L3P 35 A1L3P H10 H10 H 0 1 N N N N N N -48.844 13.603 -38.018 -6.218 0.340 1.834 H10 A1L3P 36 A1L3P H11 H11 H 0 1 N N N N N N -49.133 11.944 -38.644 -6.919 0.261 0.200 H11 A1L3P 37 A1L3P H12 H12 H 0 1 N N N N N N -47.423 12.231 -40.158 -4.779 1.049 -0.638 H12 A1L3P 38 A1L3P H14 H14 H 0 1 N N N N N N -47.108 8.145 -37.938 -1.536 -1.087 -3.275 H14 A1L3P 39 A1L3P H15 H15 H 0 1 N N N N N N -51.452 14.313 -40.218 -7.885 3.581 1.423 H15 A1L3P 40 A1L3P H16 H16 H 0 1 N N N N N N -46.778 12.341 -32.491 1.046 -4.443 1.521 H16 A1L3P 41 A1L3P H17 H17 H 0 1 N N N N N N -48.577 11.044 -31.090 3.131 -4.026 1.678 H17 A1L3P 42 A1L3P H19 H19 H 0 1 N N N N N N -53.916 14.394 -36.480 4.075 2.605 -1.982 H19 A1L3P 43 A1L3P O3 O11 O 0 1 N N N N N N -52.330 11.726 -37.132 4.994 3.560 0.555 O3 A1L3P 44 A1L3P H13 H13 H 0 1 N N N N N N -52.852 11.053 -37.553 5.661 4.187 0.243 H13 A1L3P 45 # 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 A1L3P O6 C1 DOUB N N 1 A1L3P C1 O1 SING N N 2 A1L3P C1 C7 SING N N 3 A1L3P O4 C4 DOUB N N 4 A1L3P N2 C7 SING N N 5 A1L3P N2 C3 SING N N 6 A1L3P C3 C5 SING N N 7 A1L3P C4 C5 SING N N 8 A1L3P C4 N3 SING N N 9 A1L3P C5 C6 DOUB N N 10 A1L3P N3 C2 SING N N 11 A1L3P C6 N1 SING N N 12 A1L3P C2 N1 SING N N 13 A1L3P C2 O2 DOUB N N 14 A1L3P OP2 P SING N N 15 A1L3P OP1 P DOUB N N 16 A1L3P P "O5'" SING N N 17 A1L3P N1 "C1'" SING N N 18 A1L3P "O5'" "C5'" SING N N 19 A1L3P "O4'" "C1'" SING N N 20 A1L3P "O4'" "C4'" SING N N 21 A1L3P "C1'" "C2'" SING N N 22 A1L3P "C5'" "C4'" SING N N 23 A1L3P "C4'" "C3'" SING N N 24 A1L3P "C2'" "O2'" SING N N 25 A1L3P "C2'" "C3'" SING N N 26 A1L3P "C3'" "O3'" SING N N 27 A1L3P "C4'" H1 SING N N 28 A1L3P "C5'" H2 SING N N 29 A1L3P "C5'" H3 SING N N 30 A1L3P "C1'" H4 SING N N 31 A1L3P "C2'" H5 SING N N 32 A1L3P C3 H6 SING N N 33 A1L3P C3 H7 SING N N 34 A1L3P "C3'" H8 SING N N 35 A1L3P C6 H9 SING N N 36 A1L3P C7 H10 SING N N 37 A1L3P C7 H11 SING N N 38 A1L3P N2 H12 SING N N 39 A1L3P N3 H14 SING N N 40 A1L3P O1 H15 SING N N 41 A1L3P "O2'" H16 SING N N 42 A1L3P "O3'" H17 SING N N 43 A1L3P OP2 H19 SING N N 44 A1L3P P O3 SING N N 45 A1L3P O3 H13 SING N N 46 # 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 A1L3P InChI InChI 1.06 "InChI=1S/C12H18N3O11P/c16-7(17)2-13-1-5-3-15(12(21)14-10(5)20)11-9(19)8(18)6(26-11)4-25-27(22,23)24/h3,6,8-9,11,13,18-19H,1-2,4H2,(H,16,17)(H,14,20,21)(H2,22,23,24)/t6-,8-,9-,11-/m1/s1" A1L3P InChIKey InChI 1.06 GYYYHBVNJWAMMS-PNHWDRBUSA-N A1L3P SMILES_CANONICAL CACTVS 3.385 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(CNCC(O)=O)C(=O)NC2=O" A1L3P SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=C(CNCC(O)=O)C(=O)NC2=O" A1L3P SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=C(C(=O)NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)CNCC(=O)O" A1L3P SMILES "OpenEye OEToolkits" 2.0.7 "C1=C(C(=O)NC(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)O)CNCC(=O)O" # _pdbx_chem_comp_identifier.comp_id A1L3P _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 "2-[[1-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-2,4-bis(oxidanylidene)pyrimidin-5-yl]methylamino]ethanoic acid" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id A1L3P _pdbx_chem_comp_synonyms.name "2-[[1-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]-2,4-bis(oxidanylidene)pyrimidin-5-yl]methylamino]ethanoic acid" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A1L3P "Create component" 2024-08-16 PDBJ A1L3P "Initial release" 2025-07-23 RCSB #