data_12V # _chem_comp.id 12V _chem_comp.name "(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H27 N3 O16 P2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "URIDINE DIPHOSPHO-5-THIO-N-ACETYLGLUCOSAMINE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-06-19 _chem_comp.pdbx_modified_date 2021-03-01 _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 623.419 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 12V _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 ? _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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 12V N1 N1 N 0 1 N N N 114.009 48.435 61.842 6.095 -1.171 0.526 N1 12V 1 12V C2 C2 C 0 1 N N N 114.899 47.663 61.192 6.342 -1.101 -0.795 C2 12V 2 12V O2 O2 O 0 1 N N N 114.771 47.448 59.984 6.014 -0.108 -1.415 O2 12V 3 12V N3 N3 N 0 1 N N N 115.956 47.069 61.865 6.949 -2.115 -1.439 N3 12V 4 12V C4 C4 C 0 1 N N N 116.102 47.296 63.204 7.319 -3.224 -0.767 C4 12V 5 12V O4 O4 O 0 1 N N N 117.040 46.775 63.785 7.868 -4.141 -1.349 O4 12V 6 12V C5 C5 C 0 1 N N N 115.197 48.098 63.885 7.064 -3.310 0.623 C5 12V 7 12V C6 C6 C 0 1 N N N 114.142 48.690 63.208 6.454 -2.278 1.245 C6 12V 8 12V PA PA P 0 1 N N N 110.392 54.319 62.765 0.398 2.136 -0.839 PA 12V 9 12V PB PB P 0 1 N N N 107.895 53.632 63.926 -2.199 0.791 -1.325 PB 12V 10 12V "C1'" "C1'" C 0 1 N N S 106.933 55.319 62.242 -4.610 -0.157 -0.673 "C1'" 12V 11 12V "O1'" "O1'" O 0 1 N N N 106.707 54.130 63.039 -3.272 0.175 -0.296 "O1'" 12V 12 12V O1A O1A O 0 1 N N N 110.089 55.554 62.031 0.756 2.044 -2.273 O1A 12V 13 12V C1B C1B C 0 1 N N R 112.940 49.082 61.052 5.439 -0.049 1.201 C1B 12V 14 12V O1B O1B O 0 1 N N N 107.455 52.361 64.520 -2.756 2.013 -1.947 O1B 12V 15 12V "C2'" "C2'" C 0 1 N N R 105.849 56.356 62.468 -5.538 0.008 0.534 "C2'" 12V 16 12V "N2'" "N2'" N 0 1 N N N 105.901 56.692 63.893 -5.554 1.413 0.947 "N2'" 12V 17 12V "O2'" "O2'" O 0 1 N N N 111.067 47.612 61.036 7.064 1.419 2.288 "O2'" 12V 18 12V O2A O2A O 0 1 N N N 110.891 54.365 64.167 -0.008 3.653 -0.484 O2A 12V 19 12V C2B C2B C 0 1 N N R 111.526 48.905 61.472 6.306 1.225 1.092 C2B 12V 20 12V O2B O2B O 0 1 N N N 108.326 54.737 64.800 -1.870 -0.291 -2.470 O2B 12V 21 12V "C3'" "C3'" C 0 1 N N R 104.476 55.812 62.040 -5.046 -0.855 1.691 "C3'" 12V 22 12V "O3'" "O3'" O 0 1 N N N 103.414 56.662 62.531 -5.760 -0.502 2.878 "O3'" 12V 23 12V O3A O3A O 0 1 N N N 109.034 53.404 62.804 -0.847 1.162 -0.533 O3A 12V 24 12V C3B C3B C 0 1 N N S 110.928 50.075 60.661 5.278 2.365 0.912 C3B 12V 25 12V O3B O3B O 0 1 N N N 111.040 49.863 59.213 5.369 3.297 1.991 O3B 12V 26 12V "C4'" "C4'" C 0 1 N N S 104.367 55.713 60.521 -5.267 -2.335 1.394 "C4'" 12V 27 12V "O4'" "O4'" O 0 1 N N N 103.073 55.204 60.211 -5.034 -3.098 2.580 "O4'" 12V 28 12V C4B C4B C 0 1 N N R 111.923 51.170 61.002 3.911 1.644 0.934 C4B 12V 29 12V O4B O4B O 0 1 N N N 113.153 50.493 61.308 4.203 0.288 0.534 O4B 12V 30 12V "C5'" "C5'" C 0 1 N N R 105.393 54.753 59.969 -4.305 -2.797 0.297 "C5'" 12V 31 12V "S5'" "S5'" S 0 1 N N N 107.064 54.990 60.506 -4.674 -1.885 -1.231 "S5'" 12V 32 12V C5B C5B C 0 1 N N N 111.538 51.979 62.246 2.949 2.297 -0.060 C5B 12V 33 12V O5B O5B O 0 1 N N N 111.430 53.389 61.925 1.659 1.693 0.058 O5B 12V 34 12V "C6'" "C6'" C 0 1 N N N 105.742 55.075 58.525 -4.485 -4.297 0.055 "C6'" 12V 35 12V "O6'" "O6'" O 0 1 N N N 104.639 55.691 57.882 -5.856 -4.571 -0.240 "O6'" 12V 36 12V "C7'" "C7'" C 0 1 N N N 106.570 57.764 64.291 -6.390 2.283 0.346 "C7'" 12V 37 12V "O7'" "O7'" O 0 1 N N N 107.132 58.541 63.516 -7.130 1.902 -0.536 "O7'" 12V 38 12V "C8'" "C8'" C 0 1 N N N 106.593 57.967 65.805 -6.406 3.729 0.771 "C8'" 12V 39 12V H5 H5 H 0 1 N N N 115.315 48.261 64.946 7.353 -4.190 1.179 H5 12V 40 12V H6 H6 H 0 1 N N N 113.442 49.331 63.723 6.252 -2.326 2.305 H6 12V 41 12V "H1'" "H1'" H 0 1 N N N 107.897 55.764 62.529 -4.937 0.502 -1.478 "H1'" 12V 42 12V H1B H1B H 0 1 N N N 113.056 48.853 59.982 5.251 -0.293 2.247 H1B 12V 43 12V "H2'" "H2'" H 0 1 N N N 106.078 57.249 61.868 -6.547 -0.299 0.258 "H2'" 12V 44 12V "HN2'" "HN2'" H 0 0 N N N 105.434 56.115 64.562 -4.962 1.718 1.653 "HN2'" 12V 45 12V "HO2'" "HO2'" H 0 0 N N N 110.163 47.491 61.301 7.626 2.206 2.274 "HO2'" 12V 46 12V HO2A HO2A H 0 0 N N N 110.962 55.269 64.449 -0.254 3.788 0.441 HO2A 12V 47 12V H2B H2B H 0 1 N N N 111.394 49.062 62.553 6.967 1.165 0.228 H2B 12V 48 12V HO2B HO2B H 0 0 N N N 108.260 54.467 65.708 -1.500 -1.119 -2.135 HO2B 12V 49 12V "H3'" "H3'" H 0 1 N N N 104.360 54.803 62.462 -3.982 -0.676 1.846 "H3'" 12V 50 12V "HO3'" "HO3'" H 0 0 N N N 102.575 56.311 62.257 -5.500 -1.010 3.659 "HO3'" 12V 51 12V H3B H3B H 0 1 N N N 109.906 50.321 60.985 5.429 2.868 -0.043 H3B 12V 52 12V HO3B HO3B H 0 0 N N N 110.661 50.604 58.754 6.229 3.734 2.061 HO3B 12V 53 12V "H4'" "H4'" H 0 1 N N N 104.514 56.709 60.077 -6.294 -2.488 1.062 "H4'" 12V 54 12V "HO4'" "HO4'" H 0 0 N N N 102.978 55.132 59.269 -5.156 -4.050 2.465 "HO4'" 12V 55 12V H4B H4B H 0 1 N N N 112.046 51.846 60.143 3.489 1.661 1.939 H4B 12V 56 12V "H5'" "H5'" H 0 1 N N N 105.111 53.699 60.112 -3.278 -2.596 0.603 "H5'" 12V 57 12V H5B H5B H 0 1 N N N 110.570 51.620 62.626 2.872 3.363 0.155 H5B 12V 58 12V H5BA H5BA H 0 0 N N N 112.309 51.842 63.019 3.324 2.158 -1.074 H5BA 12V 59 12V "H6'" "H6'" H 0 1 N N N 106.604 55.758 58.503 -3.864 -4.607 -0.785 "H6'" 12V 60 12V "H6'A" "H6'A" H 0 0 N N N 105.998 54.145 57.997 -4.189 -4.847 0.948 "H6'A" 12V 61 12V "HO6'" "HO6'" H 0 0 N N N 104.867 55.888 56.981 -6.044 -5.505 -0.405 "HO6'" 12V 62 12V "H8'" "H8'" H 0 1 N N N 107.167 58.874 66.045 -5.680 3.881 1.570 "H8'" 12V 63 12V "H8'A" "H8'A" H 0 0 N N N 105.563 58.076 66.176 -6.149 4.360 -0.079 "H8'A" 12V 64 12V "H8'B" "H8'B" H 0 0 N N N 107.066 57.097 66.284 -7.402 3.991 1.131 "H8'B" 12V 65 12V HN3 HN3 H 0 1 N N N 116.602 46.483 61.377 7.120 -2.049 -2.392 HN3 12V 66 # # 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 12V C1B N1 SING N N 1 12V C2 N1 SING N N 2 12V N1 C6 SING N N 3 12V O2 C2 DOUB N N 4 12V C2 N3 SING N N 5 12V N3 C4 SING N N 6 12V C4 O4 DOUB N N 7 12V C4 C5 SING N N 8 12V C6 C5 DOUB N N 9 12V C5 H5 SING N N 10 12V C6 H6 SING N N 11 12V O5B PA SING N N 12 12V O1A PA DOUB N N 13 12V PA O3A SING N N 14 12V PA O2A SING N N 15 12V O3A PB SING N N 16 12V "O1'" PB SING N N 17 12V PB O1B DOUB N N 18 12V PB O2B SING N N 19 12V "S5'" "C1'" SING N N 20 12V "C1'" "C2'" SING N N 21 12V "C1'" "O1'" SING N N 22 12V "C1'" "H1'" SING N N 23 12V C1B O4B SING N N 24 12V C1B C2B SING N N 25 12V C1B H1B SING N N 26 12V "C3'" "C2'" SING N N 27 12V "C2'" "N2'" SING N N 28 12V "C2'" "H2'" SING N N 29 12V "N2'" "C7'" SING N N 30 12V "N2'" "HN2'" SING N N 31 12V "O2'" C2B SING N N 32 12V "O2'" "HO2'" SING N N 33 12V O2A HO2A SING N N 34 12V C3B C2B SING N N 35 12V C2B H2B SING N N 36 12V O2B HO2B SING N N 37 12V "C4'" "C3'" SING N N 38 12V "C3'" "O3'" SING N N 39 12V "C3'" "H3'" SING N N 40 12V "O3'" "HO3'" SING N N 41 12V O3B C3B SING N N 42 12V C3B C4B SING N N 43 12V C3B H3B SING N N 44 12V O3B HO3B SING N N 45 12V "C5'" "C4'" SING N N 46 12V "O4'" "C4'" SING N N 47 12V "C4'" "H4'" SING N N 48 12V "O4'" "HO4'" SING N N 49 12V C4B O4B SING N N 50 12V C4B C5B SING N N 51 12V C4B H4B SING N N 52 12V "C6'" "C5'" SING N N 53 12V "C5'" "S5'" SING N N 54 12V "C5'" "H5'" SING N N 55 12V O5B C5B SING N N 56 12V C5B H5B SING N N 57 12V C5B H5BA SING N N 58 12V "O6'" "C6'" SING N N 59 12V "C6'" "H6'" SING N N 60 12V "C6'" "H6'A" SING N N 61 12V "O6'" "HO6'" SING N N 62 12V "O7'" "C7'" DOUB N N 63 12V "C7'" "C8'" SING N N 64 12V "C8'" "H8'" SING N N 65 12V "C8'" "H8'A" SING N N 66 12V "C8'" "H8'B" SING N N 67 12V N3 HN3 SING N N 68 # # 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 12V InChI InChI 1.03 "InChI=1S/C17H27N3O16P2S/c1-6(22)18-10-13(26)12(25)8(4-21)39-16(10)35-38(31,32)36-37(29,30)33-5-7-11(24)14(27)15(34-7)20-3-2-9(23)19-17(20)28/h2-3,7-8,10-16,21,24-27H,4-5H2,1H3,(H,18,22)(H,29,30)(H,31,32)(H,19,23,28)/t7-,8-,10-,11-,12-,13-,14-,15-,16+/m1/s1" 12V InChIKey InChI 1.03 JPRVHSQHWXZSNC-UBDZBXRQSA-N 12V SMILES ACDLabs 12.01 "O=P(OC1SC(C(O)C(O)C1NC(=O)C)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O" 12V SMILES_CANONICAL CACTVS 3.370 "CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)S[C@@H]1O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O" 12V SMILES CACTVS 3.370 "CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)S[CH]1O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O" 12V SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](S[C@@H]1OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)CO)O)O" 12V SMILES "OpenEye OEToolkits" 1.7.6 "CC(=O)NC1C(C(C(SC1OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)CO)O)O" # # 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 12V "SYSTEMATIC NAME" ACDLabs 12.01 "(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)" 12V "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2S,3R,4R,5S,6R)-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)thian-2-yl] [[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] 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 12V "Create component" 2012-06-19 EBI 12V "Initial release" 2012-10-19 RCSB 12V "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 12V _pdbx_chem_comp_synonyms.name "URIDINE DIPHOSPHO-5-THIO-N-ACETYLGLUCOSAMINE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##