data_GMI # _chem_comp.id GMI _chem_comp.name "[2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-5-yl]ethoxy-oxidanyl-phosphoryl]methylphosphonic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C13 H21 N4 O6 P2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2022-01-03 _chem_comp.pdbx_modified_date 2022-02-11 _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 423.342 _chem_comp.one_letter_code ? _chem_comp.three_letter_code GMI _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 7TDB _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 GMI "N1'" N1 N 0 1 Y N N 8.417 17.525 -2.383 6.062 -2.321 -0.037 "N1'" GMI 1 GMI "C2'" C1 C 0 1 Y N N 7.193 17.199 -2.816 7.023 -1.620 -0.603 "C2'" GMI 2 GMI CM2 C2 C 0 1 N N N 7.023 15.811 -3.371 8.079 -2.337 -1.403 CM2 GMI 3 GMI "N3'" N2 N 0 1 Y N N 6.127 18.011 -2.791 7.086 -0.308 -0.489 "N3'" GMI 4 GMI "C4'" C3 C 0 1 Y N N 6.264 19.259 -2.293 6.171 0.357 0.210 "C4'" GMI 5 GMI "N4'" N3 N 0 1 N N N 5.220 20.101 -2.251 6.240 1.735 0.328 "N4'" GMI 6 GMI "C5'" C4 C 0 1 Y N N 7.540 19.668 -1.815 5.139 -0.356 0.823 "C5'" GMI 7 GMI "C6'" C5 C 0 1 Y N N 8.567 18.758 -1.889 5.113 -1.730 0.676 "C6'" GMI 8 GMI "C7'" C6 C 0 1 N N N 7.737 21.061 -1.274 4.079 0.354 1.625 "C7'" GMI 9 GMI N3 N4 N 1 1 Y N N 9.157 21.434 -1.231 3.061 0.894 0.720 N3 GMI 10 GMI C2 C7 C 0 1 Y N N 9.804 21.895 -2.249 3.145 2.094 0.253 C2 GMI 11 GMI S1 S1 S 0 1 Y N N 11.442 22.204 -1.855 1.812 2.423 -0.767 S1 GMI 12 GMI C5 C8 C 0 1 Y N N 11.193 21.637 -0.195 1.180 0.803 -0.478 C5 GMI 13 GMI C4 C9 C 0 1 Y N N 9.907 21.267 -0.070 2.024 0.173 0.344 C4 GMI 14 GMI CM4 C10 C 0 1 N N N 9.296 20.723 1.192 1.805 -1.244 0.807 CM4 GMI 15 GMI C6 C11 C 0 1 N N N 12.234 21.586 0.890 -0.085 0.229 -1.061 C6 GMI 16 GMI C7 C12 C 0 1 N N N 13.262 22.695 0.643 -1.259 0.528 -0.126 C7 GMI 17 GMI O7 O1 O 0 1 N N N 12.672 23.838 1.257 -2.459 -0.017 -0.678 O7 GMI 18 GMI PA P1 P 0 1 N N N 13.135 25.323 1.083 -3.892 0.110 0.043 PA GMI 19 GMI O1A O2 O 0 1 N N N 12.069 26.182 1.700 -3.802 -0.428 1.419 O1A GMI 20 GMI O2A O3 O 0 1 N N N 14.446 25.529 1.900 -4.329 1.659 0.100 O2A GMI 21 GMI PB P2 P 0 1 N N N 13.946 27.508 -1.139 -6.756 -0.693 -0.083 PB GMI 22 GMI O1B O4 O 0 1 N N N 15.368 27.767 -0.587 -7.852 -1.529 -0.915 O1B GMI 23 GMI O2B O5 O 0 1 N N N 12.974 28.516 -0.471 -7.193 0.856 -0.026 O2B GMI 24 GMI O3B O6 O 0 1 N N N 13.952 27.706 -2.616 -6.666 -1.230 1.293 O3B GMI 25 GMI C3A C13 C 0 1 N N N 13.432 25.733 -0.718 -5.133 -0.837 -0.899 C3A GMI 26 GMI H1 H1 H 0 1 N N N 5.980 15.669 -3.691 8.907 -2.611 -0.749 H1 GMI 27 GMI H2 H2 H 0 1 N N N 7.693 15.676 -4.233 7.652 -3.237 -1.845 H2 GMI 28 GMI H3 H3 H 0 1 N N N 7.272 15.073 -2.594 8.443 -1.681 -2.194 H3 GMI 29 GMI H4 H4 H 0 1 N N N 4.411 19.649 -2.628 6.960 2.223 -0.102 H4 GMI 30 GMI H5 H5 H 0 1 N N N 5.043 20.365 -1.303 5.568 2.213 0.839 H5 GMI 31 GMI H6 H6 H 0 1 N N N 9.542 19.053 -1.531 4.330 -2.314 1.135 H6 GMI 32 GMI H7 H7 H 0 1 N N N 7.201 21.773 -1.919 3.614 -0.349 2.317 H7 GMI 33 GMI H8 H8 H 0 1 N N N 7.325 21.109 -0.255 4.535 1.169 2.188 H8 GMI 34 GMI H9 H9 H 0 1 N N N 9.369 22.064 -3.223 3.940 2.789 0.474 H9 GMI 35 GMI H10 H10 H 0 1 N N N 9.393 19.627 1.204 1.138 -1.246 1.669 H10 GMI 36 GMI H11 H11 H 0 1 N N N 9.816 21.147 2.063 1.358 -1.825 0.000 H11 GMI 37 GMI H12 H12 H 0 1 N N N 8.231 20.997 1.231 2.761 -1.687 1.087 H12 GMI 38 GMI H13 H13 H 0 1 N N N 11.755 21.737 1.869 -0.274 0.679 -2.036 H13 GMI 39 GMI H14 H14 H 0 1 N N N 12.736 20.607 0.875 0.024 -0.850 -1.174 H14 GMI 40 GMI H15 H15 H 0 1 N N N 14.226 22.450 1.113 -1.070 0.077 0.849 H15 GMI 41 GMI H16 H16 H 0 1 N N N 13.411 22.860 -0.434 -1.368 1.606 -0.013 H16 GMI 42 GMI H17 H17 H 0 1 N N N 14.287 26.147 2.604 -4.408 2.077 -0.768 H17 GMI 43 GMI H18 H18 H 0 1 N N N 15.949 27.998 -1.302 -8.741 -1.497 -0.537 H18 GMI 44 GMI H19 H19 H 0 1 N N N 12.574 29.061 -1.139 -7.272 1.275 -0.894 H19 GMI 45 GMI H20 H20 H 0 1 N N N 12.499 25.522 -1.262 -5.199 -0.441 -1.913 H20 GMI 46 GMI H21 H21 H 0 1 N N N 14.227 25.065 -1.081 -4.837 -1.885 -0.938 H21 GMI 47 # # 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 GMI CM2 "C2'" SING N N 1 GMI "C2'" "N3'" DOUB Y N 2 GMI "C2'" "N1'" SING Y N 3 GMI "N3'" "C4'" SING Y N 4 GMI O3B PB DOUB N N 5 GMI "N1'" "C6'" DOUB Y N 6 GMI "C4'" "N4'" SING N N 7 GMI "C4'" "C5'" DOUB Y N 8 GMI C2 S1 SING Y N 9 GMI C2 N3 DOUB Y N 10 GMI "C6'" "C5'" SING Y N 11 GMI S1 C5 SING Y N 12 GMI "C5'" "C7'" SING N N 13 GMI "C7'" N3 SING N N 14 GMI N3 C4 SING Y N 15 GMI PB C3A SING N N 16 GMI PB O1B SING N N 17 GMI PB O2B SING N N 18 GMI C3A PA SING N N 19 GMI C5 C4 DOUB Y N 20 GMI C5 C6 SING N N 21 GMI C4 CM4 SING N N 22 GMI C7 C6 SING N N 23 GMI C7 O7 SING N N 24 GMI PA O7 SING N N 25 GMI PA O1A DOUB N N 26 GMI PA O2A SING N N 27 GMI CM2 H1 SING N N 28 GMI CM2 H2 SING N N 29 GMI CM2 H3 SING N N 30 GMI "N4'" H4 SING N N 31 GMI "N4'" H5 SING N N 32 GMI "C6'" H6 SING N N 33 GMI "C7'" H7 SING N N 34 GMI "C7'" H8 SING N N 35 GMI C2 H9 SING N N 36 GMI CM4 H10 SING N N 37 GMI CM4 H11 SING N N 38 GMI CM4 H12 SING N N 39 GMI C6 H13 SING N N 40 GMI C6 H14 SING N N 41 GMI C7 H15 SING N N 42 GMI C7 H16 SING N N 43 GMI O2A H17 SING N N 44 GMI O1B H18 SING N N 45 GMI O2B H19 SING N N 46 GMI C3A H20 SING N N 47 GMI C3A H21 SING N N 48 # # 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 GMI SMILES ACDLabs 12.01 "O=P(O)(O)CP(=O)(O)OCCc1sc[n+](Cc2cnc(C)nc2N)c1C" GMI InChI InChI 1.03 "InChI=1S/C13H20N4O6P2S/c1-9-12(3-4-23-25(21,22)8-24(18,19)20)26-7-17(9)6-11-5-15-10(2)16-13(11)14/h5,7H,3-4,6,8H2,1-2H3,(H4-,14,15,16,18,19,20,21,22)/p+1" GMI InChIKey InChI 1.03 NSFCGDWNWBEOER-UHFFFAOYSA-O GMI SMILES_CANONICAL CACTVS 3.385 "Cc1ncc(C[n+]2csc(CCO[P](O)(=O)C[P](O)(O)=O)c2C)c(N)n1" GMI SMILES CACTVS 3.385 "Cc1ncc(C[n+]2csc(CCO[P](O)(=O)C[P](O)(O)=O)c2C)c(N)n1" GMI SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(CP(=O)(O)O)O" GMI SMILES "OpenEye OEToolkits" 2.0.7 "Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(CP(=O)(O)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 GMI "SYSTEMATIC NAME" ACDLabs 12.01 "3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonomethyl)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium" GMI "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-3-ium-5-yl]ethoxy-oxidanyl-phosphoryl]methylphosphonic acid" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site GMI "Create component" 2022-01-03 RCSB GMI "Modify coordinates" 2022-01-13 RCSB GMI "Initial release" 2022-02-16 RCSB ##