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 
# 
