data_PYI # _chem_comp.id PYI _chem_comp.name "1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-2-METHYLPYRIDINIUM" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C14 H21 N4 O7 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "PYRITHIAMIN PYROPHOSPHATE" _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2005-11-17 _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 419.287 _chem_comp.one_letter_code ? _chem_comp.three_letter_code PYI _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag Y _chem_comp.pdbx_model_coordinates_db_code 2F17 _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 PYI CM2 CM2 C 0 1 N N N 6.847 69.455 25.418 7.607 2.557 1.324 CM2 PYI 1 PYI C2A C2A C 0 1 Y N N 6.831 69.863 23.969 6.561 1.803 0.544 C2A PYI 2 PYI N1A N1A N 0 1 Y N N 7.958 69.791 23.262 5.415 2.394 0.272 N1A PYI 3 PYI C6A C6A C 0 1 Y N N 7.996 70.145 21.964 4.468 1.766 -0.411 C6A PYI 4 PYI C5A C5A C 0 1 Y N N 6.830 70.601 21.334 4.693 0.473 -0.841 C5A PYI 5 PYI C7A C7A C 0 1 N N N 6.862 71.008 19.868 3.643 -0.276 -1.621 C7A PYI 6 PYI N3 N3 N 1 1 Y N N 6.222 70.048 18.906 2.846 -1.096 -0.705 N3 PYI 7 PYI C2 C2 C 0 1 Y N N 5.941 68.776 19.293 3.171 -2.363 -0.531 C2 PYI 8 PYI C1 C1 C 0 1 Y N N 5.356 67.853 18.430 2.443 -3.167 0.325 C1 PYI 9 PYI C6 C6 C 0 1 Y N N 5.055 68.250 17.125 1.362 -2.627 1.005 C6 PYI 10 PYI C5 C5 C 0 1 Y N N 5.341 69.567 16.706 1.051 -1.292 0.796 C5 PYI 11 PYI CM6 CM6 C 0 1 N N N 5.013 69.959 15.286 -0.114 -0.659 1.511 CM6 PYI 12 PYI CM7 CM7 C 0 1 N N N 6.208 69.575 14.405 -1.351 -0.706 0.612 CM7 PYI 13 PYI OM7 OM7 O 0 1 N N N 5.794 68.604 13.443 -2.456 -0.105 1.290 OM7 PYI 14 PYI PA PA P 0 1 N N R 6.337 69.077 11.999 -3.716 -0.189 0.292 PA PYI 15 PYI O1A O1A O 0 1 N N N 6.229 67.879 11.047 -4.109 -1.732 0.051 O1A PYI 16 PYI O2A O2A O 0 1 N N N 5.452 70.231 11.458 -3.363 0.437 -1.002 O2A PYI 17 PYI O3A O3A O 0 1 N N N 7.914 69.496 12.155 -4.968 0.588 0.941 O3A PYI 18 PYI PB PB P 0 1 N N N 8.353 70.714 11.179 -6.039 0.814 -0.240 PB PYI 19 PYI O1B O1B O 0 1 N N N 9.823 70.456 10.717 -6.876 -0.542 -0.472 O1B PYI 20 PYI O2B O2B O 0 1 N N N 7.444 70.792 9.907 -7.045 2.003 0.167 O2B PYI 21 PYI O3B O3B O 0 1 N N N 8.300 72.081 11.952 -5.328 1.175 -1.488 O3B PYI 22 PYI C4 C4 C 0 1 Y N N 5.938 70.477 17.636 1.828 -0.548 -0.072 C4 PYI 23 PYI CM4 CM4 C 0 1 N N N 6.262 71.915 17.212 1.500 0.904 -0.306 CM4 PYI 24 PYI C4A C4A C 0 1 Y N N 5.644 70.667 22.116 5.918 -0.124 -0.536 C4A PYI 25 PYI N4A N4A N 0 1 N N N 4.457 71.108 21.556 6.191 -1.419 -0.945 N4A PYI 26 PYI N3A N3A N 0 1 Y N N 5.692 70.292 23.414 6.820 0.573 0.149 N3A PYI 27 PYI HM21 1HM2 H 0 0 N N N 7.638 70.037 25.945 7.465 2.379 2.390 HM21 PYI 28 PYI HM22 2HM2 H 0 0 N N N 5.904 69.515 26.010 8.598 2.215 1.027 HM22 PYI 29 PYI HM23 3HM2 H 0 0 N N N 7.252 68.419 25.494 7.514 3.624 1.119 HM23 PYI 30 PYI H6A H6A H 0 1 N N N 8.958 70.064 21.430 3.533 2.259 -0.629 H6A PYI 31 PYI H7A1 1H7A H 0 0 N N N 7.912 71.215 19.555 2.992 0.436 -2.130 H7A1 PYI 32 PYI H7A2 2H7A H 0 0 N N N 6.414 72.022 19.746 4.125 -0.918 -2.358 H7A2 PYI 33 PYI H2 H2 H 0 1 N N N 6.193 68.487 20.327 4.014 -2.776 -1.064 H2 PYI 34 PYI H1 H1 H 0 1 N N N 5.136 66.828 18.773 2.713 -4.204 0.464 H1 PYI 35 PYI H6 H6 H 0 1 N N N 4.594 67.528 16.430 0.775 -3.232 1.680 H6 PYI 36 PYI HM61 1HM6 H 0 0 N N N 4.731 71.033 15.188 -0.314 -1.204 2.434 HM61 PYI 37 PYI HM62 2HM6 H 0 0 N N N 4.053 69.521 14.927 0.124 0.379 1.747 HM62 PYI 38 PYI HM71 1HM7 H 0 0 N N N 7.081 69.229 15.006 -1.151 -0.160 -0.310 HM71 PYI 39 PYI HM72 2HM7 H 0 0 N N N 6.685 70.464 13.930 -1.589 -1.743 0.376 HM72 PYI 40 PYI H2A H2A H 0 1 N N N 5.772 70.510 10.608 ? ? ? H2A PYI 41 PYI H2B H2B H 0 1 N N N 7.701 71.506 9.335 -7.668 2.105 -0.565 H2B PYI 42 PYI H3B H3B H 0 1 N N N 8.557 72.795 11.380 ? ? ? H3B PYI 43 PYI HM41 1HM4 H 0 0 N N N 7.343 72.104 17.412 2.111 1.525 0.350 HM41 PYI 44 PYI HM42 2HM4 H 0 0 N N N 6.031 72.264 16.179 1.708 1.161 -1.345 HM42 PYI 45 PYI HM43 3HM4 H 0 0 N N N 5.775 72.611 17.934 0.446 1.078 -0.093 HM43 PYI 46 PYI H4A1 1H4A H 0 0 N N N 4.264 70.542 20.729 5.530 -1.919 -1.448 H4A1 PYI 47 PYI H4A2 2H4A H 0 0 N N N 3.606 71.155 22.117 7.045 -1.826 -0.729 H4A2 PYI 48 # # 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 PYI CM2 C2A SING N N 1 PYI CM2 HM21 SING N N 2 PYI CM2 HM22 SING N N 3 PYI CM2 HM23 SING N N 4 PYI C2A N1A DOUB Y N 5 PYI C2A N3A SING Y N 6 PYI N1A C6A SING Y N 7 PYI C6A C5A DOUB Y N 8 PYI C6A H6A SING N N 9 PYI C5A C7A SING N N 10 PYI C5A C4A SING Y N 11 PYI C7A N3 SING N N 12 PYI C7A H7A1 SING N N 13 PYI C7A H7A2 SING N N 14 PYI N3 C2 DOUB Y N 15 PYI N3 C4 SING Y N 16 PYI C2 C1 SING Y N 17 PYI C2 H2 SING N N 18 PYI C1 C6 DOUB Y N 19 PYI C1 H1 SING N N 20 PYI C6 C5 SING Y N 21 PYI C6 H6 SING N N 22 PYI C5 CM6 SING N N 23 PYI C5 C4 DOUB Y N 24 PYI CM6 CM7 SING N N 25 PYI CM6 HM61 SING N N 26 PYI CM6 HM62 SING N N 27 PYI CM7 OM7 SING N N 28 PYI CM7 HM71 SING N N 29 PYI CM7 HM72 SING N N 30 PYI OM7 PA SING N N 31 PYI PA O1A DOUB N N 32 PYI PA O2A SING N N 33 PYI PA O3A SING N N 34 PYI O2A H2A SING N N 35 PYI O3A PB SING N N 36 PYI PB O1B DOUB N N 37 PYI PB O2B SING N N 38 PYI PB O3B SING N N 39 PYI O2B H2B SING N N 40 PYI O3B H3B SING N N 41 PYI C4 CM4 SING N N 42 PYI CM4 HM41 SING N N 43 PYI CM4 HM42 SING N N 44 PYI CM4 HM43 SING N N 45 PYI C4A N4A SING N N 46 PYI C4A N3A DOUB Y N 47 PYI N4A H4A1 SING N N 48 PYI N4A H4A2 SING N N 49 # # 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 PYI SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)OCCc1ccc[n+](c1C)Cc2cnc(nc2N)C" PYI SMILES_CANONICAL CACTVS 3.341 "Cc1ncc(C[n+]2cccc(CCO[P@](O)(=O)O[P](O)(O)=O)c2C)c(N)n1" PYI SMILES CACTVS 3.341 "Cc1ncc(C[n+]2cccc(CCO[P](O)(=O)O[P](O)(O)=O)c2C)c(N)n1" PYI SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "Cc1c(ccc[n+]1Cc2cnc(nc2N)C)CCO[P@@](=O)(O)OP(=O)(O)O" PYI SMILES "OpenEye OEToolkits" 1.5.0 "Cc1c(ccc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(O)OP(=O)(O)O" PYI InChI InChI 1.03 "InChI=1S/C14H20N4O7P2/c1-10-12(5-7-24-27(22,23)25-26(19,20)21)4-3-6-18(10)9-13-8-16-11(2)17-14(13)15/h3-4,6,8H,5,7,9H2,1-2H3,(H4-,15,16,17,19,20,21,22,23)/p+1" PYI InChIKey InChI 1.03 ZHKSTKOYQKNDSJ-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 PYI "SYSTEMATIC NAME" ACDLabs 10.04 "1-[(4-amino-2-methylpyrimidin-5-yl)methyl]-3-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-2-methylpyridinium" PYI "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "2-[1-[(4-amino-2-methyl-pyrimidin-5-yl)methyl]-2-methyl-pyridin-1-ium-3-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 PYI "Create component" 2005-11-17 RCSB PYI "Modify descriptor" 2011-06-04 RCSB PYI "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id PYI _pdbx_chem_comp_synonyms.name "PYRITHIAMIN PYROPHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##