data_D2X # _chem_comp.id D2X _chem_comp.name "3-[(4-hydroxy-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H18 N3 O8 P2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2008-05-20 _chem_comp.pdbx_modified_date 2011-06-04 _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 426.299 _chem_comp.one_letter_code ? _chem_comp.three_letter_code D2X _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 3D2X _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 D2X OAJ OAJ O 0 1 N N N -1.774 -45.841 11.716 6.976 2.173 -1.060 OAJ D2X 1 D2X PAW PAW P 0 1 N N N -1.163 -44.378 11.985 6.542 0.915 -0.154 PAW D2X 2 D2X OAZ OAZ O 0 1 N N N -0.989 -44.261 13.580 7.559 -0.306 -0.409 OAZ D2X 3 D2X OAX OAX O 0 1 N N N 0.101 -44.140 11.254 6.581 1.299 1.275 OAX D2X 4 D2X OAV OAV O 0 1 N N N -2.323 -43.343 11.569 5.048 0.460 -0.546 OAV D2X 5 D2X PAU PAU P 0 1 N N R -2.024 -42.178 10.499 3.910 -0.402 0.197 PAU D2X 6 D2X OAI OAI O 0 1 N N N -2.784 -40.875 11.062 4.301 -1.963 0.148 OAI D2X 7 D2X OAY OAY O 0 1 N N N -0.575 -41.960 10.289 3.802 0.035 1.607 OAY D2X 8 D2X OAT OAT O 0 1 N N N -2.793 -42.592 9.147 2.498 -0.178 -0.543 OAT D2X 9 D2X CAS CAS C 0 1 N N N -4.184 -42.921 9.170 1.270 -0.726 -0.060 CAS D2X 10 D2X CAR CAR C 0 1 N N N -5.027 -41.678 9.459 0.128 -0.324 -0.995 CAR D2X 11 D2X CAQ CAQ C 0 1 Y N N -4.839 -40.612 8.378 -1.167 -0.902 -0.485 CAQ D2X 12 D2X CAH CAH C 0 1 Y N N -5.103 -40.655 7.014 -2.012 -0.309 0.364 CAH D2X 13 D2X CAB CAB C 0 1 N N N -5.687 -41.890 6.324 -1.764 1.062 0.936 CAB D2X 14 D2X SAP SAP S 0 1 Y N N -4.193 -39.026 8.697 -1.838 -2.475 -0.908 SAP D2X 15 D2X CAO CAO C 0 1 Y N N -4.325 -38.513 7.036 -3.184 -2.183 0.104 CAO D2X 16 D2X NAG NAG N 1 1 Y N N -4.828 -39.536 6.341 -3.080 -1.022 0.659 NAG D2X 17 D2X CAF CAF C 0 1 N N N -5.049 -39.440 4.893 -4.106 -0.518 1.575 CAF D2X 18 D2X CAE CAE C 0 1 Y N N -6.487 -39.004 4.603 -5.082 0.340 0.812 CAE D2X 19 D2X CAN CAN C 0 1 Y N N -7.341 -38.747 5.669 -4.930 1.712 0.762 CAN D2X 20 D2X NAM NAM N 0 1 Y N N -8.596 -38.379 5.480 -5.807 2.435 0.081 NAM D2X 21 D2X CAL CAL C 0 1 Y N N -9.111 -38.238 4.251 -6.817 1.864 -0.544 CAL D2X 22 D2X CAK CAK C 0 1 N N N -10.571 -37.814 4.073 -7.790 2.727 -1.305 CAK D2X 23 D2X NAC NAC N 0 1 Y N N -8.317 -38.478 3.126 -7.000 0.559 -0.521 NAC D2X 24 D2X CAD CAD C 0 1 Y N N -6.985 -38.864 3.314 -6.159 -0.232 0.136 CAD D2X 25 D2X OAA OAA O 0 1 N N N -6.246 -39.065 2.352 -6.351 -1.573 0.156 OAA D2X 26 D2X HOAJ HOAJ H 0 0 N N N -1.894 -45.968 10.782 7.867 2.501 -0.877 HOAJ D2X 27 D2X HOAZ HOAZ H 0 0 N N N -0.064 -44.238 13.797 7.586 -0.611 -1.326 HOAZ D2X 28 D2X HOAI HOAI H 0 0 N N N -2.934 -40.974 11.995 4.389 -2.318 -0.747 HOAI D2X 29 D2X HAS HAS H 0 1 N N N -4.473 -43.332 8.191 1.346 -1.813 -0.025 HAS D2X 30 D2X HASA HASA H 0 0 N N N -4.360 -43.662 9.964 1.071 -0.344 0.942 HASA D2X 31 D2X HAR HAR H 0 1 N N N -6.088 -41.968 9.491 0.053 0.763 -1.030 HAR D2X 32 D2X HARA HARA H 0 0 N N N -4.704 -41.256 10.422 0.327 -0.707 -1.997 HARA D2X 33 D2X HAB HAB H 0 1 N N N -5.827 -41.681 5.253 -2.204 1.814 0.282 HAB D2X 34 D2X HABA HABA H 0 0 N N N -4.997 -42.738 6.444 -2.217 1.131 1.925 HABA D2X 35 D2X HABB HABB H 0 0 N N N -6.657 -42.139 6.779 -0.690 1.234 1.016 HABB D2X 36 D2X HAO HAO H 0 1 N N N -4.050 -37.546 6.642 -4.005 -2.868 0.255 HAO D2X 37 D2X HAF HAF H 0 1 N N N -4.354 -38.700 4.469 -4.635 -1.358 2.025 HAF D2X 38 D2X HAFA HAFA H 0 0 N N N -4.875 -40.426 4.438 -3.634 0.076 2.357 HAFA D2X 39 D2X HAN HAN H 0 1 N N N -6.969 -38.851 6.678 -4.105 2.190 1.271 HAN D2X 40 D2X HAK HAK H 0 1 N N N -11.047 -37.712 5.060 -7.447 2.839 -2.334 HAK D2X 41 D2X HAKA HAKA H 0 0 N N N -10.611 -36.849 3.546 -8.774 2.258 -1.299 HAKA D2X 42 D2X HAKB HAKB H 0 0 N N N -11.105 -38.576 3.486 -7.852 3.708 -0.834 HAKB D2X 43 D2X H19 H19 H 0 1 N N N -6.766 -39.117 1.558 -5.914 -2.044 -0.567 H19 D2X 44 # 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 D2X OAJ PAW SING N N 1 D2X OAJ HOAJ SING N N 2 D2X PAW OAZ SING N N 3 D2X OAZ HOAZ SING N N 4 D2X OAX PAW DOUB N N 5 D2X OAV PAW SING N N 6 D2X PAU OAV SING N N 7 D2X PAU OAI SING N N 8 D2X OAI HOAI SING N N 9 D2X OAY PAU DOUB N N 10 D2X OAT PAU SING N N 11 D2X OAT CAS SING N N 12 D2X CAS CAR SING N N 13 D2X CAS HAS SING N N 14 D2X CAS HASA SING N N 15 D2X CAR HAR SING N N 16 D2X CAR HARA SING N N 17 D2X CAQ CAR SING N N 18 D2X CAQ SAP SING Y N 19 D2X CAH CAQ DOUB Y N 20 D2X CAB CAH SING N N 21 D2X CAB HAB SING N N 22 D2X CAB HABA SING N N 23 D2X CAB HABB SING N N 24 D2X CAO SAP SING Y N 25 D2X CAO HAO SING N N 26 D2X NAG CAH SING Y N 27 D2X NAG CAO DOUB Y N 28 D2X CAF NAG SING N N 29 D2X CAF HAF SING N N 30 D2X CAF HAFA SING N N 31 D2X CAE CAF SING N N 32 D2X CAE CAN DOUB Y N 33 D2X CAN HAN SING N N 34 D2X NAM CAN SING Y N 35 D2X CAL NAM DOUB Y N 36 D2X CAK CAL SING N N 37 D2X CAK HAK SING N N 38 D2X CAK HAKA SING N N 39 D2X CAK HAKB SING N N 40 D2X NAC CAL SING Y N 41 D2X NAC CAD DOUB Y N 42 D2X CAD CAE SING Y N 43 D2X OAA CAD SING N N 44 D2X OAA H19 SING N N 45 # 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 D2X SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)OCCc1sc[n+](c1C)Cc2c(nc(nc2)C)O" D2X SMILES_CANONICAL CACTVS 3.341 "Cc1ncc(C[n+]2csc(CCO[P@](O)(=O)O[P](O)(O)=O)c2C)c(O)n1" D2X SMILES CACTVS 3.341 "Cc1ncc(C[n+]2csc(CCO[P](O)(=O)O[P](O)(O)=O)c2C)c(O)n1" D2X SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "Cc1c(sc[n+]1Cc2cnc(nc2O)C)CCO[P@@](=O)(O)OP(=O)(O)O" D2X SMILES "OpenEye OEToolkits" 1.5.0 "Cc1c(sc[n+]1Cc2cnc(nc2O)C)CCOP(=O)(O)OP(=O)(O)O" D2X InChI InChI 1.03 "InChI=1S/C12H17N3O8P2S/c1-8-11(3-4-22-25(20,21)23-24(17,18)19)26-7-15(8)6-10-5-13-9(2)14-12(10)16/h5,7H,3-4,6H2,1-2H3,(H3-,13,14,16,17,18,19,20,21)/p+1" D2X InChIKey InChI 1.03 FBFAORFKQFQJGN-UHFFFAOYSA-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 D2X "SYSTEMATIC NAME" ACDLabs 10.04 "3-[(4-hydroxy-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium" D2X "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "2-[3-[(4-hydroxy-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-3-ium-5-yl]ethyl 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 D2X "Create component" 2008-05-20 RCSB D2X "Modify descriptor" 2011-06-04 RCSB #