data_MJL
# 
_chem_comp.id                                    MJL 
_chem_comp.name                                  "(2~{S},3~{S},4~{R},5~{R},6~{R})-4,5-diacetamido-6-[[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxane-2-carboxylic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C19 H28 N4 O18 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         UDP-2,3-diacetamido-2,3-dideoxy-alpha-D-glucuronate 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-05-26 
_chem_comp.pdbx_modified_date                    2023-09-08 
_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                        662.389 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     MJL 
_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        8SY9 
_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.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 
MJL N1    N1  N 0 1 N N N -16.512 74.299 0.909  6.133  1.351  -0.632 N1    MJL 1  
MJL N3    N2  N 0 1 N N N -18.694 74.419 -0.092 6.860  2.600  1.211  N3    MJL 2  
MJL C4    C1  C 0 1 N N N -18.142 75.135 -1.073 7.131  3.652  0.412  C4    MJL 3  
MJL C5    C2  C 0 1 N N N -16.865 75.435 -1.063 6.885  3.551  -0.978 C5    MJL 4  
MJL C6    C3  C 0 1 N N N -16.055 75.058 -0.107 6.389  2.398  -1.475 C6    MJL 5  
MJL C2    C4  C 0 1 N N N -17.910 73.989 0.903  6.366  1.462  0.688  C2    MJL 6  
MJL O2    O1  O 0 1 N N N -18.442 73.325 1.803  6.126  0.521  1.420  O2    MJL 7  
MJL O4    O2  O 0 1 N N N -18.910 75.521 -1.944 7.578  4.682  0.884  O4    MJL 8  
MJL PA    P1  P 0 1 N N N -12.637 77.984 2.029  0.774  -2.321 1.121  PA    MJL 9  
MJL PB    P2  P 0 1 N N N -10.047 78.285 2.843  -2.161 -2.032 0.820  PB    MJL 10 
MJL "O'P" O3  O 0 1 N N N -10.527 78.742 8.909  -4.139 3.150  3.255  "O'P" MJL 11 
MJL "O'Q" O4  O 0 1 N N N -10.044 80.876 8.548  -5.305 1.341  3.754  "O'Q" MJL 12 
MJL "C1'" C5  C 0 1 N N R -9.201  80.084 4.624  -4.477 -0.763 0.412  "C1'" MJL 13 
MJL O1A   O5  O 0 1 N N N -12.253 77.402 0.681  0.695  -3.799 1.143  O1A   MJL 14 
MJL O1B   O6  O 0 1 N N N -9.168  78.869 1.827  -2.392 -2.157 2.277  O1B   MJL 15 
MJL C1C   C6  C 0 1 N N R -15.695 73.856 2.019  5.595  0.099  -1.172 C1C   MJL 16 
MJL "C2'" C7  C 0 1 N N R -7.684  80.130 4.845  -5.104 -0.035 -0.780 "C2'" MJL 17 
MJL "N2'" N3  N 0 1 N N N -6.970  80.153 3.575  -4.752 -0.731 -2.020 "N2'" MJL 18 
MJL O2A   O7  O 0 1 N N N -13.920 78.746 1.910  1.018  -1.775 2.616  O2A   MJL 19 
MJL O2B   O8  O 0 1 N N N -10.065 76.790 2.855  -2.566 -3.409 0.092  O2B   MJL 20 
MJL C2C   C8  C 0 1 N N R -14.551 72.950 1.671  6.581  -1.063 -0.919 C2C   MJL 21 
MJL O2C   O9  O 0 1 N N N -14.888 71.568 1.574  7.363  -1.318 -2.088 O2C   MJL 22 
MJL "C3'" C9  C 0 1 N N R -7.282  78.951 5.699  -4.572 1.401  -0.830 "C3'" MJL 23 
MJL "N3'" N4  N 0 1 N N N -5.871  78.945 5.936  -5.225 2.128  -1.922 "N3'" MJL 24 
MJL O3A   O10 O 0 1 N N N -11.496 78.890 2.583  -0.605 -1.718 0.549  O3A   MJL 25 
MJL O3B   O11 O 0 1 N N N -9.600  78.760 4.281  -3.060 -0.831 0.235  O3B   MJL 26 
MJL C3C   C10 C 0 1 N N S -13.553 73.198 2.810  5.667  -2.269 -0.606 C3C   MJL 27 
MJL O3C   O12 O 0 1 N N N -13.715 72.306 3.901  5.858  -3.306 -1.570 O3C   MJL 28 
MJL "C4'" C11 C 0 1 N N S -7.990  79.080 7.009  -4.878 2.093  0.502  "C4'" MJL 29 
MJL "O4'" O13 O 0 1 N N N -7.720  77.862 7.714  -4.323 3.410  0.494  "O4'" MJL 30 
MJL C4C   C12 C 0 1 N N R -13.830 74.639 3.249  4.238  -1.692 -0.705 C4C   MJL 31 
MJL O4C   O14 O 0 1 N N N -15.097 75.027 2.635  4.393  -0.277 -0.465 O4C   MJL 32 
MJL "C5'" C13 C 0 1 N N S -9.505  79.304 6.840  -4.259 1.283  1.644  "C5'" MJL 33 
MJL "O5'" O15 O 0 1 N N N -9.806  80.353 5.883  -4.773 -0.050 1.614  "O5'" MJL 34 
MJL C5C   C14 C 0 1 N N N -12.701 75.472 2.709  3.335  -2.319 0.359  C5C   MJL 35 
MJL O5C   O16 O 0 1 N N N -12.806 76.834 3.105  1.994  -1.862 0.176  O5C   MJL 36 
MJL "C6'" C15 C 0 1 N N N -10.085 79.662 8.180  -4.606 1.926  2.962  "C6'" MJL 37 
MJL "C7'" C16 C 0 1 N N N -5.888  80.881 3.318  -5.490 -1.779 -2.438 "C7'" MJL 38 
MJL "O7'" O17 O 0 1 N N N -5.388  81.597 4.159  -6.445 -2.146 -1.787 "O7'" MJL 39 
MJL "C8'" C17 C 0 1 N N N -5.282  80.803 1.909  -5.127 -2.495 -3.713 "C8'" MJL 40 
MJL O43   O18 O 0 1 N N N -5.371  77.193 4.596  -3.518 3.534  -2.096 O43   MJL 41 
MJL C41   C18 C 0 1 N N N -5.003  78.079 5.334  -4.610 3.184  -2.489 C41   MJL 42 
MJL C42   C19 C 0 1 N N N -3.523  78.261 5.571  -5.281 3.932  -3.612 C42   MJL 43 
MJL H1    H1  H 0 1 N N N -19.672 74.209 -0.100 7.022  2.663  2.165  H1    MJL 44 
MJL H2    H2  H 0 1 N N N -16.465 76.018 -1.879 7.096  4.383  -1.633 H2    MJL 45 
MJL H3    H3  H 0 1 N N N -15.017 75.356 -0.132 6.196  2.302  -2.534 H3    MJL 46 
MJL H4    H4  H 0 1 N N N -10.809 79.104 9.741  -4.388 3.521  4.113  H4    MJL 47 
MJL H5    H5  H 0 1 N N N -9.499  80.816 3.858  -4.884 -1.771 0.477  H5    MJL 48 
MJL H6    H6  H 0 1 N N N -16.332 73.346 2.757  5.392  0.203  -2.238 H6    MJL 49 
MJL H7    H7  H 0 1 N N N -7.451  81.051 5.400  -6.188 -0.018 -0.666 H7    MJL 50 
MJL H8    H8  H 0 1 N N N -7.322  79.575 2.838  -3.988 -0.437 -2.540 H8    MJL 51 
MJL H9    H9  H 0 1 N N N -14.230 78.708 1.013  1.080  -0.812 2.678  H9    MJL 52 
MJL H10   H10 H 0 1 N N N -9.484  76.460 2.179  -2.440 -3.399 -0.866 H10   MJL 53 
MJL H11   H11 H 0 1 N N N -14.098 73.293 0.729  7.225  -0.840 -0.069 H11   MJL 54 
MJL H12   H12 H 0 1 N N N -14.112 71.067 1.352  8.000  -2.039 -1.985 H12   MJL 55 
MJL H13   H13 H 0 1 N N N -7.592  78.019 5.203  -3.495 1.385  -0.995 H13   MJL 56 
MJL H14   H14 H 0 1 N N N -5.499  79.614 6.580  -6.099 1.848  -2.236 H14   MJL 57 
MJL H15   H15 H 0 1 N N N -12.531 73.136 2.409  5.859  -2.642 0.400  H15   MJL 58 
MJL H16   H16 H 0 1 N N N -13.073 72.506 4.572  6.756  -3.662 -1.592 H16   MJL 59 
MJL H17   H17 H 0 1 N N N -7.571  79.934 7.562  -5.958 2.154  0.641  H17   MJL 60 
MJL H18   H18 H 0 1 N N N -8.148  77.885 8.562  -4.479 3.908  1.308  H18   MJL 61 
MJL H19   H19 H 0 1 N N N -13.876 74.705 4.346  3.827  -1.866 -1.700 H19   MJL 62 
MJL H20   H20 H 0 1 N N N -9.957  78.360 6.501  -3.176 1.258  1.526  H20   MJL 63 
MJL H21   H21 H 0 1 N N N -12.715 75.420 1.610  3.364  -3.405 0.266  H21   MJL 64 
MJL H22   H22 H 0 1 N N N -11.750 75.066 3.083  3.686  -2.030 1.349  H22   MJL 65 
MJL H23   H23 H 0 1 N N N -4.404  81.462 1.850  -4.247 -2.026 -4.155 H23   MJL 66 
MJL H24   H24 H 0 1 N N N -4.978  79.767 1.698  -4.911 -3.540 -3.494 H24   MJL 67 
MJL H25   H25 H 0 1 N N N -6.031  81.123 1.170  -5.961 -2.435 -4.413 H25   MJL 68 
MJL H26   H26 H 0 1 N N N -2.964  77.508 4.997  -4.638 4.749  -3.941 H26   MJL 69 
MJL H27   H27 H 0 1 N N N -3.221  79.268 5.247  -5.460 3.253  -4.446 H27   MJL 70 
MJL H28   H28 H 0 1 N N N -3.306  78.140 6.643  -6.232 4.336  -3.263 H28   MJL 71 
# 
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 
MJL O4    C4    DOUB N N 1  
MJL C4    C5    SING N N 2  
MJL C4    N3    SING N N 3  
MJL C5    C6    DOUB N N 4  
MJL C6    N1    SING N N 5  
MJL N3    C2    SING N N 6  
MJL O1A   PA    DOUB N N 7  
MJL C2    N1    SING N N 8  
MJL C2    O2    DOUB N N 9  
MJL N1    C1C   SING N N 10 
MJL O2C   C2C   SING N N 11 
MJL C2C   C1C   SING N N 12 
MJL C2C   C3C   SING N N 13 
MJL O1B   PB    DOUB N N 14 
MJL "C8'" "C7'" SING N N 15 
MJL O2A   PA    SING N N 16 
MJL C1C   O4C   SING N N 17 
MJL PA    O3A   SING N N 18 
MJL PA    O5C   SING N N 19 
MJL O3A   PB    SING N N 20 
MJL O4C   C4C   SING N N 21 
MJL C5C   O5C   SING N N 22 
MJL C5C   C4C   SING N N 23 
MJL C3C   C4C   SING N N 24 
MJL C3C   O3C   SING N N 25 
MJL PB    O2B   SING N N 26 
MJL PB    O3B   SING N N 27 
MJL "C7'" "N2'" SING N N 28 
MJL "C7'" "O7'" DOUB N N 29 
MJL "N2'" "C2'" SING N N 30 
MJL O3B   "C1'" SING N N 31 
MJL O43   C41   DOUB N N 32 
MJL "C1'" "C2'" SING N N 33 
MJL "C1'" "O5'" SING N N 34 
MJL "C2'" "C3'" SING N N 35 
MJL C41   C42   SING N N 36 
MJL C41   "N3'" SING N N 37 
MJL "C3'" "N3'" SING N N 38 
MJL "C3'" "C4'" SING N N 39 
MJL "O5'" "C5'" SING N N 40 
MJL "C5'" "C4'" SING N N 41 
MJL "C5'" "C6'" SING N N 42 
MJL "C4'" "O4'" SING N N 43 
MJL "C6'" "O'Q" DOUB N N 44 
MJL "C6'" "O'P" SING N N 45 
MJL N3    H1    SING N N 46 
MJL C5    H2    SING N N 47 
MJL C6    H3    SING N N 48 
MJL "O'P" H4    SING N N 49 
MJL "C1'" H5    SING N N 50 
MJL C1C   H6    SING N N 51 
MJL "C2'" H7    SING N N 52 
MJL "N2'" H8    SING N N 53 
MJL O2A   H9    SING N N 54 
MJL O2B   H10   SING N N 55 
MJL C2C   H11   SING N N 56 
MJL O2C   H12   SING N N 57 
MJL "C3'" H13   SING N N 58 
MJL "N3'" H14   SING N N 59 
MJL C3C   H15   SING N N 60 
MJL O3C   H16   SING N N 61 
MJL "C4'" H17   SING N N 62 
MJL "O4'" H18   SING N N 63 
MJL C4C   H19   SING N N 64 
MJL "C5'" H20   SING N N 65 
MJL C5C   H21   SING N N 66 
MJL C5C   H22   SING N N 67 
MJL "C8'" H23   SING N N 68 
MJL "C8'" H24   SING N N 69 
MJL "C8'" H25   SING N N 70 
MJL C42   H26   SING N N 71 
MJL C42   H27   SING N N 72 
MJL C42   H28   SING N N 73 
# 
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 
MJL SMILES           ACDLabs              12.01 "O=C1C=CN(C(=O)N1)C1OC(COP(=O)(O)OP(=O)(O)OC2OC(C(O)C(NC(C)=O)C2NC(C)=O)C(=O)O)C(O)C1O"                                                                                                                                                                                                        
MJL InChI            InChI                1.06  "InChI=1S/C19H28N4O18P2/c1-6(24)20-10-11(21-7(2)25)18(39-15(13(10)28)17(30)31)40-43(35,36)41-42(33,34)37-5-8-12(27)14(29)16(38-8)23-4-3-9(26)22-19(23)32/h3-4,8,10-16,18,27-29H,5H2,1-2H3,(H,20,24)(H,21,25)(H,30,31)(H,33,34)(H,35,36)(H,22,26,32)/t8-,10-,11-,12-,13+,14-,15+,16-,18-/m1/s1" 
MJL InChIKey         InChI                1.06  GZLIMKLKXDFTJR-LTMKHLKMSA-N                                                                                                                                                                                                                                                                    
MJL SMILES_CANONICAL CACTVS               3.385 "CC(=O)N[C@H]1[C@H](O)[C@H](O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@@H]1NC(C)=O)C(O)=O"                                                                                                                                                                
MJL SMILES           CACTVS               3.385 "CC(=O)N[CH]1[CH](O)[CH](O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH]1NC(C)=O)C(O)=O"                                                                                                                                                                           
MJL SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(=O)N[C@@H]1[C@H]([C@H](O[C@@H]([C@H]1O)C(=O)O)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C"                                                                                                                                                                
MJL SMILES           "OpenEye OEToolkits" 2.0.7 "CC(=O)NC1C(C(OC(C1O)C(=O)O)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C"                                                                                                                                                                                                        
# 
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 
MJL "SYSTEMATIC NAME" ACDLabs              12.01 "(2S,3S,4R,5R,6R)-4,5-diacetamido-6-{[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3-hydroxyoxane-2-carboxylic acid (non-preferred name)" 
MJL "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S},3~{S},4~{R},5~{R},6~{R})-4,5-diacetamido-6-[[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxane-2-carboxylic acid"    
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      MJL 
_pdbx_chem_comp_synonyms.name         UDP-2,3-diacetamido-2,3-dideoxy-alpha-D-glucuronate 
_pdbx_chem_comp_synonyms.provenance   PUBCHEM 
_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 
MJL "Create component" 2023-05-26 RCSB 
MJL "Initial release"  2023-09-13 RCSB 
# 
