data_MJ3
# 
_chem_comp.id                                    MJ3 
_chem_comp.name                                  "(2~{S},3~{S},4~{R},5~{S},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-mannuronic acid" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-05-25 
_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                     MJ3 
_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        8SY0 
_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 
MJ3 N1    N1  N 0 1 N N N -17.155 74.290 0.791  -6.331 -1.242 -0.140 N1    MJ3 1  
MJ3 C2    C1  C 0 1 N N N -18.547 73.979 0.839  -6.631 -2.387 -0.781 C2    MJ3 2  
MJ3 O2    O1  O 0 1 N N N -19.077 73.272 1.747  -6.468 -2.460 -1.984 O2    MJ3 3  
MJ3 N3    N2  N 0 1 N N N -19.288 74.423 -0.173 -7.107 -3.451 -0.109 N3    MJ3 4  
MJ3 C4    C2  C 0 1 N N N -18.749 75.161 -1.166 -7.293 -3.386 1.224  C4    MJ3 5  
MJ3 O4    O2  O 0 1 N N N -19.508 75.550 -2.051 -7.724 -4.349 1.833  O4    MJ3 6  
MJ3 C5    C3  C 0 1 N N N -17.473 75.482 -1.205 -6.982 -2.188 1.911  C5    MJ3 7  
MJ3 C6    C4  C 0 1 N N N -16.686 75.066 -0.234 -6.500 -1.137 1.214  C6    MJ3 8  
MJ3 PA    P1  P 0 1 N N N -13.459 78.355 1.637  -0.868 2.587  0.739  PA    MJ3 9  
MJ3 PB    P2  P 0 1 N N N -10.752 78.555 2.350  2.045  2.213  0.343  PB    MJ3 10 
MJ3 "O'P" O3  O 0 1 N N N -10.920 79.014 8.406  4.115  -2.538 3.477  "O'P" MJ3 11 
MJ3 "O'Q" O4  O 0 1 N N N -10.300 81.215 8.217  5.315  -0.689 3.621  "O'Q" MJ3 12 
MJ3 "C1'" C5  C 0 1 N N R -9.814  80.200 4.087  4.330  0.864  0.029  "C1'" MJ3 13 
MJ3 O1A   O5  O 0 1 N N N -13.004 77.726 0.356  -0.780 4.048  0.520  O1A   MJ3 14 
MJ3 O1B   O6  O 0 1 N N N -10.003 79.267 1.262  2.351  2.565  1.748  O1B   MJ3 15 
MJ3 C1C   C6  C 0 1 N N R -16.251 73.883 1.884  -5.814 -0.100 -0.898 C1C   MJ3 16 
MJ3 "C2'" C7  C 0 1 N N S -8.275  80.332 4.034  4.892  -0.054 -1.060 "C2'" MJ3 17 
MJ3 "N2'" N3  N 0 1 N N N -8.022  81.737 4.192  6.355  -0.072 -0.977 "N2'" MJ3 18 
MJ3 O2A   O7  O 0 1 N N N -14.574 79.301 1.623  -1.040 2.289  2.312  O2A   MJ3 19 
MJ3 O2B   O8  O 0 1 N N N -10.748 77.046 2.250  2.421  3.452  -0.614 O2B   MJ3 20 
MJ3 C2C   C8  C 0 1 N N R -15.043 73.060 1.534  -6.779 1.101  -0.786 C2C   MJ3 21 
MJ3 O2C   O9  O 0 1 N N N -15.329 71.675 1.436  -7.618 1.178  -1.940 O2C   MJ3 22 
MJ3 "C3'" C9  C 0 1 N N R -7.710  79.423 5.128  4.350  -1.471 -0.852 "C3'" MJ3 23 
MJ3 "N3'" N4  N 0 1 N N N -6.271  79.444 5.241  4.942  -2.372 -1.844 "N3'" MJ3 24 
MJ3 O3A   O10 O 0 1 N N N -12.258 79.081 2.360  0.476  1.882  0.202  O3A   MJ3 25 
MJ3 O3B   O11 O 0 1 N N N -10.117 78.880 3.792  2.907  0.923  -0.086 O3B   MJ3 26 
MJ3 C3C   C10 C 0 1 N N S -14.114 73.406 2.656  -5.844 2.329  -0.714 C3C   MJ3 27 
MJ3 O3C   O12 O 0 1 N N N -14.380 72.510 3.746  -6.077 3.201  -1.822 O3C   MJ3 28 
MJ3 "C4'" C11 C 0 1 N N S -8.346  79.603 6.497  4.720  -1.946 0.556  "C4'" MJ3 29 
MJ3 "O4'" O13 O 0 1 N N N -7.982  78.480 7.338  4.157  -3.239 0.787  "O4'" MJ3 30 
MJ3 C4C   C12 C 0 1 N N R -14.469 74.872 3.049  -4.424 1.724  -0.791 C4C   MJ3 31 
MJ3 O4C   O14 O 0 1 N N N -15.709 75.113 2.396  -4.575 0.367  -0.321 O4C   MJ3 32 
MJ3 "C5'" C13 C 0 1 N N S -9.875  79.633 6.408  4.164  -0.956 1.582  "C5'" MJ3 33 
MJ3 "O5'" O15 O 0 1 N N N -10.313 80.508 5.403  4.683  0.348  1.314  "O5'" MJ3 34 
MJ3 C5C   C14 C 0 1 N N N -13.465 75.842 2.506  -3.465 2.500  0.114  C5C   MJ3 35 
MJ3 O5C   O16 O 0 1 N N N -13.896 77.196 2.638  -2.137 2.000  -0.060 O5C   MJ3 36 
MJ3 "C6'" C15 C 0 1 N N N -10.421 80.005 7.758  4.574  -1.384 2.968  "C6'" MJ3 37 
MJ3 "C7'" C16 C 0 1 N N N -8.268  82.688 3.227  7.077  0.885  -1.593 "C7'" MJ3 38 
MJ3 "O7'" O17 O 0 1 N N N -8.546  82.443 2.072  6.515  1.762  -2.216 "O7'" MJ3 39 
MJ3 "C8'" C17 C 0 1 N N N -8.140  84.128 3.638  8.581  0.867  -1.508 "C8'" MJ3 40 
MJ3 O43   O18 O 0 1 N N N -5.921  77.558 4.063  3.220  -3.765 -1.706 O43   MJ3 41 
MJ3 C41   C18 C 0 1 N N N -5.486  78.500 4.697  4.294  -3.498 -2.204 C41   MJ3 42 
MJ3 C42   C19 C 0 1 N N N -4.021  78.670 4.830  4.903  -4.425 -3.224 C42   MJ3 43 
MJ3 H1    H1  H 0 1 N N N -20.264 74.205 -0.198 -7.319 -4.269 -0.587 H1    MJ3 44 
MJ3 H2    H2  H 0 1 N N N -17.079 76.075 -2.017 -7.124 -2.116 2.979  H2    MJ3 45 
MJ3 H3    H3  H 0 1 N N N -15.643 75.345 -0.247 -6.257 -0.215 1.720  H3    MJ3 46 
MJ3 H4    H4  H 0 1 N N N -11.186 79.303 9.271  4.405  -2.771 4.369  H4    MJ3 47 
MJ3 H5    H5  H 0 1 N N N -10.254 80.882 3.344  4.746  1.865  -0.089 H5    MJ3 48 
MJ3 H6    H6  H 0 1 N N N -16.827 73.368 2.667  -5.666 -0.374 -1.943 H6    MJ3 49 
MJ3 H7    H7  H 0 1 N N N -7.919  79.983 3.053  4.588  0.314  -2.040 H7    MJ3 50 
MJ3 H8    H8  H 0 1 N N N -7.641  82.046 5.063  6.804  -0.773 -0.479 H8    MJ3 51 
MJ3 H9    H9  H 0 1 N N N -14.892 79.403 0.734  -1.104 1.349  2.529  H9    MJ3 52 
MJ3 H10   H10 H 0 1 N N N -10.252 76.780 1.484  2.246  3.292  -1.551 H10   MJ3 53 
MJ3 H11   H11 H 0 1 N N N -14.619 73.429 0.588  -7.380 1.025  0.120  H11   MJ3 54 
MJ3 H12   H12 H 0 1 N N N -14.535 71.202 1.214  -8.244 1.915  -1.923 H12   MJ3 55 
MJ3 H13   H13 H 0 1 N N N -7.976  78.402 4.818  3.266  -1.467 -0.965 H13   MJ3 56 
MJ3 H14   H14 H 0 1 N N N -5.841  80.193 5.745  5.801  -2.159 -2.242 H14   MJ3 57 
MJ3 H15   H15 H 0 1 N N N -13.066 73.349 2.328  -5.982 2.860  0.228  H15   MJ3 58 
MJ3 H16   H16 H 0 1 N N N -13.800 72.712 4.471  -6.973 3.562  -1.856 H16   MJ3 59 
MJ3 H17   H17 H 0 1 N N N -7.991  80.544 6.942  5.805  -1.999 0.650  H17   MJ3 60 
MJ3 H18   H18 H 0 1 N N N -8.376  78.585 8.196  4.352  -3.602 1.662  H18   MJ3 61 
MJ3 H19   H19 H 0 1 N N N -14.552 74.961 4.142  -4.064 1.731  -1.820 H19   MJ3 62 
MJ3 H20   H20 H 0 1 N N N -10.214 78.613 6.175  3.076  -0.935 1.515  H20   MJ3 63 
MJ3 H21   H21 H 0 1 N N N -13.303 75.624 1.440  -3.493 3.557  -0.150 H21   MJ3 64 
MJ3 H22   H22 H 0 1 N N N -12.519 75.716 3.054  -3.767 2.376  1.154  H22   MJ3 65 
MJ3 H23   H23 H 0 1 N N N -8.331  84.776 2.770  8.901  0.012  -0.912 H23   MJ3 66 
MJ3 H24   H24 H 0 1 N N N -8.871  84.350 4.429  9.001  0.788  -2.511 H24   MJ3 67 
MJ3 H25   H25 H 0 1 N N N -7.124  84.312 4.016  8.930  1.787  -1.040 H25   MJ3 68 
MJ3 H26   H26 H 0 1 N N N -3.507  77.858 4.295  4.573  -4.134 -4.222 H26   MJ3 69 
MJ3 H27   H27 H 0 1 N N N -3.724  79.638 4.400  5.990  -4.363 -3.168 H27   MJ3 70 
MJ3 H28   H28 H 0 1 N N N -3.744  78.641 5.894  4.586  -5.448 -3.021 H28   MJ3 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 
MJ3 O4    C4    DOUB N N 1  
MJ3 C5    C4    SING N N 2  
MJ3 C5    C6    DOUB N N 3  
MJ3 C4    N3    SING N N 4  
MJ3 C6    N1    SING N N 5  
MJ3 N3    C2    SING N N 6  
MJ3 O1A   PA    DOUB N N 7  
MJ3 N1    C2    SING N N 8  
MJ3 N1    C1C   SING N N 9  
MJ3 C2    O2    DOUB N N 10 
MJ3 O1B   PB    DOUB N N 11 
MJ3 O2C   C2C   SING N N 12 
MJ3 C2C   C1C   SING N N 13 
MJ3 C2C   C3C   SING N N 14 
MJ3 O2A   PA    SING N N 15 
MJ3 PA    O3A   SING N N 16 
MJ3 PA    O5C   SING N N 17 
MJ3 C1C   O4C   SING N N 18 
MJ3 "O7'" "C7'" DOUB N N 19 
MJ3 O2B   PB    SING N N 20 
MJ3 PB    O3A   SING N N 21 
MJ3 PB    O3B   SING N N 22 
MJ3 O4C   C4C   SING N N 23 
MJ3 C5C   O5C   SING N N 24 
MJ3 C5C   C4C   SING N N 25 
MJ3 C3C   C4C   SING N N 26 
MJ3 C3C   O3C   SING N N 27 
MJ3 "C7'" "C8'" SING N N 28 
MJ3 "C7'" "N2'" SING N N 29 
MJ3 O3B   "C1'" SING N N 30 
MJ3 "C2'" "C1'" SING N N 31 
MJ3 "C2'" "N2'" SING N N 32 
MJ3 "C2'" "C3'" SING N N 33 
MJ3 O43   C41   DOUB N N 34 
MJ3 "C1'" "O5'" SING N N 35 
MJ3 C41   C42   SING N N 36 
MJ3 C41   "N3'" SING N N 37 
MJ3 "C3'" "N3'" SING N N 38 
MJ3 "C3'" "C4'" SING N N 39 
MJ3 "O5'" "C5'" SING N N 40 
MJ3 "C5'" "C4'" SING N N 41 
MJ3 "C5'" "C6'" SING N N 42 
MJ3 "C4'" "O4'" SING N N 43 
MJ3 "C6'" "O'Q" DOUB N N 44 
MJ3 "C6'" "O'P" SING N N 45 
MJ3 N3    H1    SING N N 46 
MJ3 C5    H2    SING N N 47 
MJ3 C6    H3    SING N N 48 
MJ3 "O'P" H4    SING N N 49 
MJ3 "C1'" H5    SING N N 50 
MJ3 C1C   H6    SING N N 51 
MJ3 "C2'" H7    SING N N 52 
MJ3 "N2'" H8    SING N N 53 
MJ3 O2A   H9    SING N N 54 
MJ3 O2B   H10   SING N N 55 
MJ3 C2C   H11   SING N N 56 
MJ3 O2C   H12   SING N N 57 
MJ3 "C3'" H13   SING N N 58 
MJ3 "N3'" H14   SING N N 59 
MJ3 C3C   H15   SING N N 60 
MJ3 O3C   H16   SING N N 61 
MJ3 "C4'" H17   SING N N 62 
MJ3 "O4'" H18   SING N N 63 
MJ3 C4C   H19   SING N N 64 
MJ3 "C5'" H20   SING N N 65 
MJ3 C5C   H21   SING N N 66 
MJ3 C5C   H22   SING N N 67 
MJ3 "C8'" H23   SING N N 68 
MJ3 "C8'" H24   SING N N 69 
MJ3 "C8'" H25   SING N N 70 
MJ3 C42   H26   SING N N 71 
MJ3 C42   H27   SING N N 72 
MJ3 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 
MJ3 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"                                                                                                                                                                                                        
MJ3 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" 
MJ3 InChIKey         InChI                1.06  GZLIMKLKXDFTJR-ZVWGYSLJSA-N                                                                                                                                                                                                                                                                    
MJ3 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"                                                                                                                                                                 
MJ3 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"                                                                                                                                                                           
MJ3 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"                                                                                                                                                               
MJ3 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 
MJ3 "SYSTEMATIC NAME" ACDLabs              12.01 "(2S,3S,4R,5S,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)" 
MJ3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S},3~{S},4~{R},5~{S},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"    
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
MJ3 "Create component" 2023-05-25 RCSB 
MJ3 "Initial release"  2023-09-13 RCSB 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      MJ3 
_pdbx_chem_comp_synonyms.name         "UDP-2,3-diacetamido-2,3-dideoxy-alpha-D-mannuronic acid" 
_pdbx_chem_comp_synonyms.provenance   PUBCHEM 
_pdbx_chem_comp_synonyms.type         ? 
# 
