data_GBO # _chem_comp.id GBO _chem_comp.name "(2E,6E)-3,7-dimethyl-8-({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)octa-2,6-dien-1-yl trihydrogen diphosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H35 N3 O9 P2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms Biotin-GPP _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2008-10-15 _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 555.519 _chem_comp.one_letter_code ? _chem_comp.three_letter_code GBO _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 3EU5 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # # 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 GBO O2 O2 O 0 1 N N N 54.796 -43.036 7.611 9.667 -3.273 -1.360 O2 GBO 1 GBO P1 P1 P 0 1 N N N 54.157 -42.406 6.279 9.442 -2.926 0.195 P1 GBO 2 GBO O8 O8 O 0 1 N N N 53.285 -41.235 6.897 9.006 -4.259 0.985 O8 GBO 3 GBO O1 O1 O 0 1 N N N 55.173 -42.042 5.272 10.701 -2.401 0.770 O1 GBO 4 GBO O3 O3 O 0 1 N N N 53.112 -43.485 5.749 8.284 -1.816 0.336 O3 GBO 5 GBO P2 P2 P 0 1 N N R 52.720 -43.748 4.195 8.217 -0.230 0.065 P2 GBO 6 GBO O4 O4 O 0 1 N N N 51.790 -44.876 4.277 8.982 0.549 1.248 O4 GBO 7 GBO O9 O9 O 0 1 N N N 52.323 -42.537 3.401 8.865 0.078 -1.229 O9 GBO 8 GBO O5 O5 O 0 1 N N N 54.148 -44.310 3.811 6.678 0.241 0.019 O5 GBO 9 GBO C1 C1 C 0 1 N N N 54.705 -44.390 2.531 6.281 1.575 -0.307 C1 GBO 10 GBO C2 C2 C 0 1 N N N 56.002 -44.864 2.654 4.779 1.678 -0.259 C2 GBO 11 GBO C3 C3 C 0 1 N N N 56.735 -45.211 1.548 4.134 2.298 -1.216 C3 GBO 12 GBO C4 C4 C 0 1 N N N 56.092 -45.046 0.144 4.899 3.016 -2.298 C4 GBO 13 GBO C5 C5 C 0 1 N N N 58.163 -45.742 1.610 2.627 2.294 -1.235 C5 GBO 14 GBO C6 C6 C 0 1 N N N 58.505 -46.600 2.819 2.105 3.563 -0.559 C6 GBO 15 GBO C7 C7 C 0 1 N N N 59.624 -47.362 2.502 0.598 3.559 -0.578 C7 GBO 16 GBO C8 C8 C 0 1 N N N 60.223 -48.336 3.269 -0.071 3.608 0.547 C8 GBO 17 GBO C9 C9 C 0 1 N N N 59.595 -48.674 4.619 0.660 3.535 1.863 C9 GBO 18 GBO C10 C10 C 0 1 N N N 61.444 -49.126 2.757 -1.573 3.736 0.525 C10 GBO 19 GBO N1 N1 N 0 1 N N N 60.817 -50.398 2.467 -2.178 2.406 0.628 N1 GBO 20 GBO C11 C11 C 0 1 N N N 61.350 -51.575 2.192 -3.519 2.274 0.629 C11 GBO 21 GBO O6 O6 O 0 1 N N N 62.547 -51.844 2.093 -4.225 3.257 0.544 O6 GBO 22 GBO C12 C12 C 0 1 N N N 60.271 -52.676 1.932 -4.142 0.906 0.734 C12 GBO 23 GBO C13 C13 C 0 1 N N N 59.196 -52.897 3.051 -5.667 1.037 0.712 C13 GBO 24 GBO C14 C14 C 0 1 N N N 58.066 -53.791 2.523 -6.299 -0.352 0.820 C14 GBO 25 GBO C15 C15 C 0 1 N N N 56.677 -53.264 2.898 -7.823 -0.222 0.798 C15 GBO 26 GBO C16 C16 C 0 1 N N S 55.578 -54.266 2.423 -8.455 -1.611 0.905 C16 GBO 27 GBO S1 S1 S 0 1 N N N 56.140 -55.706 1.387 -8.151 -2.586 -0.624 S1 GBO 28 GBO C17 C17 C 0 1 N N N 54.428 -56.118 0.878 -9.654 -3.629 -0.444 C17 GBO 29 GBO C18 C18 C 0 1 N N R 53.772 -54.723 0.654 -10.672 -2.653 0.178 C18 GBO 30 GBO C19 C19 C 0 1 N N S 54.489 -53.606 1.500 -9.993 -1.510 0.947 C19 GBO 31 GBO N2 N2 N 0 1 N N N 55.148 -52.759 0.465 -10.414 -0.297 0.228 N2 GBO 32 GBO C20 C20 C 0 1 N N N 54.917 -53.245 -0.749 -11.207 -0.648 -0.794 C20 GBO 33 GBO O7 O7 O 0 1 N N N 55.364 -52.749 -1.785 -11.699 0.159 -1.558 O7 GBO 34 GBO N3 N3 N 0 1 N N N 54.132 -54.329 -0.714 -11.411 -1.973 -0.897 N3 GBO 35 GBO HO2 HO2 H 0 1 N N N 55.730 -43.160 7.487 8.881 -3.623 -1.803 HO2 GBO 36 GBO HO8 HO8 H 0 1 N N N 53.111 -41.419 7.813 9.658 -4.972 0.944 HO8 GBO 37 GBO HO4 HO4 H 0 1 N N N 51.589 -45.185 3.402 8.609 0.394 2.126 HO4 GBO 38 GBO H1 H1 H 0 1 N N N 54.113 -45.075 1.907 6.717 2.269 0.412 H1 GBO 39 GBO H1A H1A H 0 1 N N N 54.706 -43.399 2.054 6.631 1.823 -1.309 H1A GBO 40 GBO H2 H2 H 0 1 N N N 56.442 -44.961 3.636 4.233 1.241 0.565 H2 GBO 41 GBO H4 H4 H 0 1 N N N 54.997 -45.007 0.244 5.173 2.308 -3.080 H4 GBO 42 GBO H4A H4A H 0 1 N N N 56.451 -44.114 -0.316 4.277 3.803 -2.722 H4A GBO 43 GBO H4B H4B H 0 1 N N N 56.372 -45.900 -0.490 5.802 3.456 -1.874 H4B GBO 44 GBO H5 H5 H 0 1 N N N 58.322 -46.360 0.714 2.277 2.261 -2.267 H5 GBO 45 GBO H5A H5A H 0 1 N N N 58.810 -44.855 1.679 2.260 1.419 -0.699 H5A GBO 46 GBO H6 H6 H 0 1 N N N 58.721 -45.958 3.686 2.455 3.596 0.473 H6 GBO 47 GBO H6A H6A H 0 1 N N N 57.658 -47.254 3.075 2.473 4.438 -1.095 H6A GBO 48 GBO H7 H7 H 0 1 N N N 60.077 -47.167 1.541 0.070 3.516 -1.519 H7 GBO 49 GBO H9 H9 H 0 1 N N N 60.384 -48.755 5.381 0.979 4.535 2.157 H9 GBO 50 GBO H9A H9A H 0 1 N N N 58.890 -47.879 4.905 -0.004 3.126 2.625 H9A GBO 51 GBO H9B H9B H 0 1 N N N 59.058 -49.631 4.544 1.533 2.891 1.758 H9B GBO 52 GBO H10 H10 H 0 1 N N N 61.906 -48.667 1.870 -1.897 4.349 1.367 H10 GBO 53 GBO H10A H10A H 0 0 N N N 62.286 -49.179 3.463 -1.884 4.206 -0.408 H10A GBO 54 GBO HN1 HN1 H 0 1 N N N 59.817 -50.383 2.476 -1.614 1.620 0.696 HN1 GBO 55 GBO H12 H12 H 0 1 N N N 59.731 -52.388 1.018 -3.818 0.293 -0.107 H12 GBO 56 GBO H12A H12A H 0 0 N N N 60.829 -53.622 1.875 -3.831 0.436 1.667 H12A GBO 57 GBO H13 H13 H 0 1 N N N 59.668 -53.382 3.918 -5.991 1.649 1.554 H13 GBO 58 GBO H13A H13A H 0 0 N N N 58.778 -51.924 3.348 -5.978 1.506 -0.221 H13A GBO 59 GBO H14 H14 H 0 1 N N N 58.138 -53.833 1.426 -5.975 -0.965 -0.021 H14 GBO 60 GBO H14A H14A H 0 0 N N N 58.183 -54.785 2.980 -5.988 -0.822 1.753 H14A GBO 61 GBO H15 H15 H 0 1 N N N 56.615 -53.148 3.990 -8.148 0.391 1.639 H15 GBO 62 GBO H15A H15A H 0 0 N N N 56.515 -52.292 2.408 -8.134 0.248 -0.135 H15A GBO 63 GBO H16 H16 H 0 1 N N N 55.212 -54.602 3.404 -8.079 -2.139 1.781 H16 GBO 64 GBO H17 H17 H 0 1 N N N 54.414 -56.723 -0.041 -10.000 -3.980 -1.416 H17 GBO 65 GBO H17A H17A H 0 0 N N N 53.895 -56.725 1.625 -9.464 -4.470 0.223 H17A GBO 66 GBO H18 H18 H 0 1 N N N 52.701 -54.802 0.893 -11.358 -3.190 0.833 H18 GBO 67 GBO H19 H19 H 0 1 N N N 53.805 -53.040 2.150 -10.347 -1.486 1.978 H19 GBO 68 GBO HN2 HN2 H 0 1 N N N 55.688 -51.940 0.658 -10.159 0.610 0.457 HN2 GBO 69 GBO HN3 HN3 H 0 1 N N N 53.824 -54.817 -1.531 -11.955 -2.408 -1.573 HN3 GBO 70 # # 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 GBO P1 O2 SING N N 1 GBO O2 HO2 SING N N 2 GBO O1 P1 DOUB N N 3 GBO O3 P1 SING N N 4 GBO P1 O8 SING N N 5 GBO O8 HO8 SING N N 6 GBO P2 O3 SING N N 7 GBO O9 P2 DOUB N N 8 GBO O5 P2 SING N N 9 GBO P2 O4 SING N N 10 GBO O4 HO4 SING N N 11 GBO C1 O5 SING N N 12 GBO C1 C2 SING N N 13 GBO C1 H1 SING N N 14 GBO C1 H1A SING N N 15 GBO C3 C2 DOUB N N 16 GBO C2 H2 SING N E 17 GBO C4 C3 SING N N 18 GBO C3 C5 SING N N 19 GBO C4 H4 SING N N 20 GBO C4 H4A SING N N 21 GBO C4 H4B SING N N 22 GBO C5 C6 SING N N 23 GBO C5 H5 SING N N 24 GBO C5 H5A SING N N 25 GBO C7 C6 SING N N 26 GBO C6 H6 SING N N 27 GBO C6 H6A SING N N 28 GBO C7 C8 DOUB N E 29 GBO C7 H7 SING N N 30 GBO C10 C8 SING N N 31 GBO C8 C9 SING N N 32 GBO C9 H9 SING N N 33 GBO C9 H9A SING N N 34 GBO C9 H9B SING N N 35 GBO N1 C10 SING N N 36 GBO C10 H10 SING N N 37 GBO C10 H10A SING N N 38 GBO C11 N1 SING N N 39 GBO N1 HN1 SING N N 40 GBO C12 C11 SING N N 41 GBO O6 C11 DOUB N N 42 GBO C12 C13 SING N N 43 GBO C12 H12 SING N N 44 GBO C12 H12A SING N N 45 GBO C14 C13 SING N N 46 GBO C13 H13 SING N N 47 GBO C13 H13A SING N N 48 GBO C14 C15 SING N N 49 GBO C14 H14 SING N N 50 GBO C14 H14A SING N N 51 GBO C16 C15 SING N N 52 GBO C15 H15 SING N N 53 GBO C15 H15A SING N N 54 GBO S1 C16 SING N N 55 GBO C19 C16 SING N N 56 GBO C16 H16 SING N N 57 GBO C17 S1 SING N N 58 GBO C18 C17 SING N N 59 GBO C17 H17 SING N N 60 GBO C17 H17A SING N N 61 GBO N3 C18 SING N N 62 GBO C18 C19 SING N N 63 GBO C18 H18 SING N N 64 GBO N2 C19 SING N N 65 GBO C19 H19 SING N N 66 GBO C20 N2 SING N N 67 GBO N2 HN2 SING N N 68 GBO O7 C20 DOUB N N 69 GBO C20 N3 SING N N 70 GBO N3 HN3 SING N N 71 # # 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 GBO SMILES ACDLabs 10.04 "O=C1NC2C(SCC2N1)CCCCC(=O)NCC(=C/CCC(=C/COP(=O)(O)OP(=O)(O)O)/C)/C" GBO SMILES_CANONICAL CACTVS 3.341 "C\C(CC\C=C(/C)CNC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12)=C/CO[P@](O)(=O)O[P](O)(O)=O" GBO SMILES CACTVS 3.341 "CC(CCC=C(C)CNC(=O)CCCC[CH]1SC[CH]2NC(=O)N[CH]12)=CCO[P](O)(=O)O[P](O)(O)=O" GBO SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C/C(=C\CO[P@@](=O)(O)OP(=O)(O)O)/CC\C=C(/C)\CNC(=O)CCCC[C@H]1[C@@H]2[C@H](CS1)NC(=O)N2" GBO SMILES "OpenEye OEToolkits" 1.5.0 "CC(=CCOP(=O)(O)OP(=O)(O)O)CCC=C(C)CNC(=O)CCCCC1C2C(CS1)NC(=O)N2" GBO InChI InChI 1.03 "InChI=1S/C20H35N3O9P2S/c1-14(10-11-31-34(29,30)32-33(26,27)28)6-5-7-15(2)12-21-18(24)9-4-3-8-17-19-16(13-35-17)22-20(25)23-19/h7,10,16-17,19H,3-6,8-9,11-13H2,1-2H3,(H,21,24)(H,29,30)(H2,22,23,25)(H2,26,27,28)/b14-10+,15-7+/t16-,17-,19-/m0/s1" GBO InChIKey InChI 1.03 XZJFCDBLIMGOSX-VRLLXNLQSA-N # # 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 GBO "SYSTEMATIC NAME" ACDLabs 10.04 "(2E,6E)-3,7-dimethyl-8-({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)octa-2,6-dien-1-yl trihydrogen diphosphate" GBO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2E,6E)-8-[5-[(3aR,6S,6aS)-2-oxo-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-6-yl]pentanoylamino]-3,7-dimethyl-octa-2,6-dienyl] phosphono 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 GBO "Create component" 2008-10-15 PDBJ GBO "Modify descriptor" 2011-06-04 RCSB GBO "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id GBO _pdbx_chem_comp_synonyms.name Biotin-GPP _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##