data_Y4H
# 
_chem_comp.id                                    Y4H 
_chem_comp.name                                  "Agrocinopine D-like (C2-C2 linked; with an alpha and beta-D-glucopyranose)" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C12 H23 O14 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "Agrocinopine D-like; [(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] [(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate; D-glucose-2-phosphate-2-glucose" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-06-09 
_chem_comp.pdbx_modified_date                    2024-01-19 
_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                        422.276 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y4H 
_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        8CAY 
_chem_comp.pdbx_subcomponent_list                "GLC BNX" 
_chem_comp.pdbx_processing_site                  PDBE 
# 
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_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_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 
Y4H C1  C5  C 0 1 N N S N N N 10.335 -24.391 16.234 -3.415 -1.334 0.240  C1  GLC 1  
Y4H C2  C6  C 0 1 N N R N N N 10.909 -23.701 17.487 -2.615 -0.098 -0.178 C2  GLC 2  
Y4H C3  C7  C 0 1 N N S N N N 12.016 -24.542 18.110 -3.317 1.157  0.350  C3  GLC 3  
Y4H C4  C1  C 0 1 N N S N N N 11.522 -25.962 18.353 -4.753 1.187  -0.181 C4  GLC 4  
Y4H C5  C2  C 0 1 N N R N N N 11.047 -26.552 17.029 -5.471 -0.099 0.237  C5  GLC 5  
Y4H C6  C3  C 0 1 N N N N N N 10.534 -27.973 17.131 -6.887 -0.104 -0.340 C6  GLC 6  
Y4H O1  O1  O 0 1 N N N N N N 11.261 -24.314 15.193 -3.446 -1.422 1.666  O1  GLC 7  
Y4H O2  O8  O 0 1 N N N N N N 11.405 -22.301 17.229 -1.297 -0.174 0.369  O2  GLC 8  
Y4H O3  O2  O 0 1 N N N N N N 12.453 -23.985 19.351 -2.617 2.320  -0.098 O3  GLC 9  
Y4H O4  O3  O 0 1 N N N N N N 12.551 -26.754 18.946 -5.440 2.316  0.363  O4  GLC 10 
Y4H O5  O4  O 0 1 N N N N N N 9.966  -25.750 16.516 -4.750 -1.228 -0.260 O5  GLC 11 
Y4H O6  O5  O 0 1 N N N N N N 9.637  -28.140 18.216 -7.596 -1.246 0.145  O6  GLC 12 
Y4H OAN O6  O 0 1 N N N N N N 9.381  -21.417 18.451 0.056  -1.533 -1.430 OAN BNX 13 
Y4H PAM P1  P 0 1 N N N N N N 10.758 -21.109 17.919 0.031  -0.191 -0.541 PAM BNX 14 
Y4H OAO O7  O 0 1 N N N N N N 10.853 -19.834 17.104 0.033  0.991  -1.432 OAO BNX 15 
Y4H OA2 O9  O 0 1 N N N N N N 11.605 -20.909 19.299 1.332  -0.150 0.407  O2  BNX 16 
Y4H C21 C4  C 0 1 N N R N N N 12.753 -20.040 19.390 2.663  -0.050 -0.103 C2  BNX 17 
Y4H C31 C8  C 0 1 N N S N N N 13.933 -20.910 19.807 3.474  -1.272 0.338  C3  BNX 18 
Y4H O31 O10 O 0 1 N N N N N N 14.274 -21.811 18.758 2.904  -2.454 -0.229 O3  BNX 19 
Y4H C41 C9  C 0 1 N N S N N N 15.138 -20.073 20.218 4.918  -1.116 -0.147 C4  BNX 20 
Y4H O41 O11 O 0 1 N N N N N N 16.135 -20.923 20.760 5.701  -2.216 0.321  O4  BNX 21 
Y4H C51 C10 C 0 1 N N R N N N 14.706 -19.052 21.271 5.494  0.192  0.402  C5  BNX 22 
Y4H C61 C11 C 0 1 N N N N N N 15.801 -18.106 21.695 6.916  0.385  -0.128 C6  BNX 23 
Y4H O61 O12 O 0 1 N N N N N N 16.371 -17.480 20.570 7.496  1.544  0.475  O6  BNX 24 
Y4H O51 O13 O 0 1 N N N N N N 13.654 -18.244 20.722 4.676  1.285  -0.020 O5  BNX 25 
Y4H C11 C12 C 0 1 N N R N N N 12.446 -18.973 20.437 3.326  1.217  0.444  C1  BNX 26 
Y4H O11 O14 O 0 1 N N N N N N 11.675 -17.859 20.144 2.607  2.365  -0.010 O1  BNX 27 
Y4H H1  H6  H 0 1 N N N N N N 9.429  -23.838 15.947 -2.944 -2.228 -0.169 H1  GLC 28 
Y4H H2  H7  H 0 1 N N N N N N 10.094 -23.634 18.223 -2.557 -0.052 -1.266 H2  GLC 29 
Y4H H3  H8  H 0 1 N N N N N N 12.859 -24.583 17.405 -3.331 1.136  1.440  H3  GLC 30 
Y4H H4  H1  H 0 1 N N N N N N 10.660 -25.913 19.035 -4.738 1.260  -1.268 H4  GLC 31 
Y4H H5  H2  H 0 1 N N N N N N 11.887 -26.534 16.319 -5.521 -0.149 1.325  H5  GLC 32 
Y4H H61 H3  H 0 1 N N N N N N 10.013 -28.230 16.197 -7.408 0.804  -0.033 H61 GLC 33 
Y4H H62 H4  H 0 1 N N N N N N 11.390 -28.650 17.271 -6.836 -0.143 -1.428 H62 GLC 34 
Y4H HO1 H9  H 0 1 N N N N N N 11.483 -23.404 15.033 -3.938 -2.183 2.003  HO1 GLC 35 
Y4H HO3 H10 H 0 1 N N N N N N 13.142 -24.527 19.717 -3.007 3.153  0.200  HO3 GLC 36 
Y4H HO4 H11 H 0 1 N N N N N N 12.822 -26.359 19.766 -6.357 2.398  0.069  HO4 GLC 37 
Y4H HO6 H12 H 0 1 N N N N N N 9.339  -29.042 18.245 -8.503 -1.314 -0.181 HO6 GLC 38 
Y4H H7  H13 H 0 1 N N N N N N 8.776  -20.737 18.178 0.056  -2.349 -0.910 H1A BNX 39 
Y4H H6  H5  H 0 1 N N N N N N 12.964 -19.563 18.422 2.634  -0.006 -1.192 H2  BNX 40 
Y4H H8  H14 H 0 1 N N N N N N 13.620 -21.493 20.686 3.460  -1.345 1.426  H3  BNX 41 
Y4H H9  H15 H 0 1 N N N N N N 15.010 -22.348 19.028 3.368  -3.268 0.010  HO3 BNX 42 
Y4H H10 H16 H 0 1 N N N N N N 15.523 -19.539 19.337 4.935  -1.094 -1.237 H4  BNX 43 
Y4H H11 H17 H 0 1 N N N N N N 16.888 -20.404 21.017 6.628  -2.182 0.050  HO4 BNX 44 
Y4H H12 H18 H 0 1 N N N N N N 14.340 -19.593 22.156 5.514  0.152  1.491  H5  BNX 45 
Y4H H13 H19 H 0 1 N N N N N N 16.580 -18.669 22.230 7.517  -0.491 0.117  H61 BNX 46 
Y4H H14 H20 H 0 1 N N N N N N 15.380 -17.339 22.362 6.887  0.515  -1.210 H62 BNX 47 
Y4H H15 H21 H 0 1 N N N N N N 17.058 -16.888 20.851 8.399  1.728  0.185  HO6 BNX 48 
Y4H H16 H22 H 0 1 N N N N N N 12.083 -19.468 21.350 3.317  1.190  1.534  H1  BNX 49 
Y4H H17 H23 H 0 1 N N N N N N 11.597 -17.315 20.919 2.972  3.206  0.299  HO1 BNX 50 
# 
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 
Y4H O1  C1  SING N N 1  
Y4H C1  O5  SING N N 2  
Y4H C1  C2  SING N N 3  
Y4H O5  C5  SING N N 4  
Y4H C5  C6  SING N N 5  
Y4H C5  C4  SING N N 6  
Y4H OAO PAM DOUB N N 7  
Y4H C6  O6  SING N N 8  
Y4H O2  C2  SING N N 9  
Y4H O2  PAM SING N N 10 
Y4H C2  C3  SING N N 11 
Y4H PAM OAN SING N N 12 
Y4H PAM OA2 SING N N 13 
Y4H C3  C4  SING N N 14 
Y4H C3  O3  SING N N 15 
Y4H C4  O4  SING N N 16 
Y4H O31 C31 SING N N 17 
Y4H OA2 C21 SING N N 18 
Y4H C21 C31 SING N N 19 
Y4H C21 C11 SING N N 20 
Y4H C31 C41 SING N N 21 
Y4H O11 C11 SING N N 22 
Y4H C41 O41 SING N N 23 
Y4H C41 C51 SING N N 24 
Y4H C11 O51 SING N N 25 
Y4H O61 C61 SING N N 26 
Y4H O51 C51 SING N N 27 
Y4H C51 C61 SING N N 28 
Y4H C4  H4  SING N N 29 
Y4H C5  H5  SING N N 30 
Y4H C6  H61 SING N N 31 
Y4H C6  H62 SING N N 32 
Y4H C21 H6  SING N N 33 
Y4H C1  H1  SING N N 34 
Y4H C2  H2  SING N N 35 
Y4H C3  H3  SING N N 36 
Y4H O1  HO1 SING N N 37 
Y4H O3  HO3 SING N N 38 
Y4H O4  HO4 SING N N 39 
Y4H O6  HO6 SING N N 40 
Y4H OAN H7  SING N N 41 
Y4H C31 H8  SING N N 42 
Y4H O31 H9  SING N N 43 
Y4H C41 H10 SING N N 44 
Y4H O41 H11 SING N N 45 
Y4H C51 H12 SING N N 46 
Y4H C61 H13 SING N N 47 
Y4H C61 H14 SING N N 48 
Y4H O61 H15 SING N N 49 
Y4H C11 H16 SING N N 50 
Y4H O11 H17 SING N N 51 
# 
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 
Y4H InChI            InChI                1.06  "InChI=1S/C12H23O14P/c13-1-3-5(15)7(17)9(11(19)23-3)25-27(21,22)26-10-8(18)6(16)4(2-14)24-12(10)20/h3-20H,1-2H2,(H,21,22)/t3-,4-,5-,6-,7+,8+,9-,10-,11-,12+/m1/s1" 
Y4H InChIKey         InChI                1.06  DCDHSOINTWUWCZ-BTLHAWITSA-N                                                                                                                                        
Y4H SMILES_CANONICAL CACTVS               3.385 "OC[C@H]1O[C@H](O)[C@H](O[P](O)(=O)O[C@H]2[C@H](O)O[C@H](CO)[C@@H](O)[C@@H]2O)[C@@H](O)[C@@H]1O"                                                                   
Y4H SMILES           CACTVS               3.385 "OC[CH]1O[CH](O)[CH](O[P](O)(=O)O[CH]2[CH](O)O[CH](CO)[CH](O)[CH]2O)[CH](O)[CH]1O"                                                                                 
Y4H SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O)OP(=O)(O)O[C@@H]2[C@H]([C@@H]([C@H](O[C@@H]2O)CO)O)O)O)O)O"                                                               
Y4H SMILES           "OpenEye OEToolkits" 2.0.7 "C(C1C(C(C(C(O1)O)OP(=O)(O)OC2C(C(C(OC2O)CO)O)O)O)O)O"                                                                                                             
# 
_pdbx_chem_comp_identifier.comp_id           Y4H 
_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~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] [(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen 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 
Y4H "Create component"   2023-06-09 PDBE 
Y4H "Other modification" 2023-12-03 PDBE 
Y4H "Modify name"        2023-12-05 PDBE 
Y4H "Initial release"    2024-01-24 RCSB 
# 
loop_
_pdbx_chem_comp_synonyms.ordinal 
_pdbx_chem_comp_synonyms.comp_id 
_pdbx_chem_comp_synonyms.name 
_pdbx_chem_comp_synonyms.provenance 
_pdbx_chem_comp_synonyms.type 
1 Y4H "Agrocinopine D-like"                                                                                                                                                                    AUTHOR ? 
2 Y4H "[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] [(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate" PDB    ? 
3 Y4H D-glucose-2-phosphate-2-glucose                                                                                                                                                          AUTHOR ? 
# 
