data_R1T # _chem_comp.id R1T _chem_comp.name "2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H23 N3 O8 P2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "2-[(1R)-1-HYDROXYETHYL]-3-DEAZA-THDP" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2007-06-18 _chem_comp.pdbx_modified_date 2021-03-01 _chem_comp.pdbx_ambiguous_flag ? _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 467.371 _chem_comp.one_letter_code ? _chem_comp.three_letter_code R1T _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details "Corina V3.40" _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 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 R1T "N1'" "N1'" N 0 1 Y N N -20.848 -10.387 17.297 3.704 -2.414 1.094 "N1'" R1T 1 R1T "C2'" "C2'" C 0 1 Y N N -21.310 -9.970 18.488 4.761 -3.167 0.861 "C2'" R1T 2 R1T CM2 CM2 C 0 1 N N N -22.018 -10.949 19.385 4.942 -4.439 1.649 CM2 R1T 3 R1T "N3'" "N3'" N 0 1 Y N N -21.146 -8.696 18.891 5.662 -2.839 -0.042 "N3'" R1T 4 R1T "C4'" "C4'" C 0 1 Y N N -20.498 -7.765 18.087 5.534 -1.724 -0.756 "C4'" R1T 5 R1T "N4'" "N4'" N 0 1 N N N -20.351 -6.488 18.535 6.484 -1.382 -1.704 "N4'" R1T 6 R1T "C5'" "C5'" C 0 1 Y N N -19.991 -8.188 16.782 4.426 -0.904 -0.534 "C5'" R1T 7 R1T "C6'" "C6'" C 0 1 Y N N -20.194 -9.541 16.443 3.507 -1.289 0.423 "C6'" R1T 8 R1T "C7'" "C7'" C 0 1 N N N -19.205 -7.273 15.776 4.238 0.369 -1.318 "C7'" R1T 9 R1T C3 C3 C 0 1 Y N N -19.993 -6.028 15.253 3.043 1.116 -0.784 C3 R1T 10 R1T C2 C2 C 0 1 Y N N -19.698 -4.775 15.690 3.135 1.995 0.215 C2 R1T 11 R1T S1 S1 S 0 1 Y N N -20.735 -3.732 14.816 1.545 2.662 0.563 S1 R1T 12 R1T C5 C5 C 0 1 Y N N -21.616 -4.935 13.869 0.824 1.681 -0.706 C5 R1T 13 R1T C4 C4 C 0 1 Y N N -20.991 -6.136 14.258 1.768 0.947 -1.296 C4 R1T 14 R1T CM4 CM4 C 0 1 N N N -21.396 -7.487 13.620 1.470 0.001 -2.431 CM4 R1T 15 R1T C6 C6 C 0 1 N N N -22.702 -4.654 12.876 -0.638 1.675 -1.074 C6 R1T 16 R1T C7 C7 C 0 1 N N N -24.074 -4.554 13.575 -1.368 0.615 -0.247 C7 R1T 17 R1T O7 O7 O 0 1 N N N -25.042 -4.479 12.540 -2.754 0.610 -0.596 O7 R1T 18 R1T PA PA P 0 1 N N S -26.480 -4.030 13.122 -3.825 -0.384 0.082 PA R1T 19 R1T O1A O1A O 0 1 N N N -26.908 -4.884 14.274 -3.781 -0.227 1.553 O1A R1T 20 R1T O2A O2A O 0 1 N N N -27.506 -4.242 11.937 -3.467 -1.904 -0.307 O2A R1T 21 R1T O3A O3A O 0 1 N N N -26.546 -2.477 13.596 -5.301 -0.026 -0.453 O3A R1T 22 R1T PB PB P 0 1 N N N -25.917 -1.348 12.541 -6.788 -0.321 0.089 PB R1T 23 R1T O1B O1B O 0 1 N N N -26.421 -1.622 11.102 -6.847 -0.046 1.542 O1B R1T 24 R1T O2B O2B O 0 1 N N N -26.439 0.047 13.063 -7.837 0.628 -0.680 O2B R1T 25 R1T O3B O3B O 0 1 N N N -24.377 -1.326 12.573 -7.162 -1.863 -0.181 O3B R1T 26 R1T CP1 CP1 C 0 1 N N R -18.601 -4.307 16.676 4.407 2.361 0.937 CP1 R1T 27 R1T CP2 CP2 C 0 1 N N N -18.224 -2.828 16.383 4.875 3.743 0.477 CP2 R1T 28 R1T OP1 OP1 O 0 1 N N N -19.023 -4.475 18.010 4.166 2.383 2.345 OP1 R1T 29 R1T HP1 HP1 H 0 1 N N N -18.264 -4.513 18.580 3.490 3.019 2.619 HP1 R1T 30 R1T H1 H1 H 0 1 N N N -17.704 -4.928 16.534 5.177 1.623 0.711 H1 R1T 31 R1T H61 1H6 H 0 1 N N N -22.487 -3.701 12.370 -1.068 2.655 -0.871 H61 R1T 32 R1T H62 2H6 H 0 1 N N N -22.736 -5.478 12.149 -0.744 1.444 -2.135 H62 R1T 33 R1T H71 1H7 H 0 1 N N N -24.251 -5.437 14.207 -0.938 -0.365 -0.450 H71 R1T 34 R1T H72 2H7 H 0 1 N N N -24.124 -3.673 14.232 -1.262 0.846 0.814 H72 R1T 35 R1T H2A H2A H 0 1 N N N -28.389 -4.285 12.286 -3.476 -2.080 -1.258 H2A R1T 36 R1T H2B H2B H 0 1 N N N -26.544 0.013 14.007 -8.755 0.505 -0.403 H2B R1T 37 R1T H3B H3B H 0 1 N N N -24.041 -1.321 11.684 -7.143 -2.115 -1.115 H3B R1T 38 R1T HM41 1HM4 H 0 0 N N N -21.492 -7.365 12.531 1.314 -1.002 -2.036 HM41 R1T 39 R1T HM42 2HM4 H 0 0 N N N -20.625 -8.241 13.838 0.571 0.331 -2.951 HM42 R1T 40 R1T HM43 3HM4 H 0 0 N N N -22.359 -7.816 14.038 2.309 -0.009 -3.126 HM43 R1T 41 R1T "H7'1" "1H7'" H 0 0 N N N -18.307 -6.905 16.293 5.128 0.990 -1.222 "H7'1" R1T 42 R1T "H7'2" "2H7'" H 0 0 N N N -18.992 -7.896 14.895 4.075 0.128 -2.369 "H7'2" R1T 43 R1T "H6'" "H6'" H 0 1 N N N -19.829 -9.915 15.498 2.637 -0.679 0.622 "H6'" R1T 44 R1T HM21 1HM2 H 0 0 N N N -22.191 -11.888 18.839 4.459 -5.263 1.124 HM21 R1T 45 R1T HM22 2HM2 H 0 0 N N N -21.398 -11.149 20.271 6.006 -4.650 1.757 HM22 R1T 46 R1T HM23 3HM2 H 0 0 N N N -22.983 -10.526 19.700 4.493 -4.323 2.635 HM23 R1T 47 R1T "H4'1" "1H4'" H 0 0 N N N -20.315 -6.487 19.534 7.290 -1.913 -1.797 "H4'1" R1T 48 R1T "H4'2" "2H4'" H 0 0 N N N -19.503 -6.103 18.171 6.342 -0.612 -2.277 "H4'2" R1T 49 R1T HP21 1HP2 H 0 0 N N N -18.135 -2.277 17.331 4.104 4.481 0.702 HP21 R1T 50 R1T HP22 2HP2 H 0 0 N N N -17.264 -2.794 15.848 5.795 4.007 0.999 HP22 R1T 51 R1T HP23 3HP2 H 0 0 N N N -19.007 -2.366 15.763 5.058 3.726 -0.597 HP23 R1T 52 # # 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 R1T "N1'" "C2'" SING Y N 1 R1T "N1'" "C6'" DOUB Y N 2 R1T "C2'" "N3'" DOUB Y N 3 R1T "C2'" CM2 SING N N 4 R1T CM2 HM21 SING N N 5 R1T CM2 HM22 SING N N 6 R1T CM2 HM23 SING N N 7 R1T "N3'" "C4'" SING Y N 8 R1T "C4'" "C5'" DOUB Y N 9 R1T "C4'" "N4'" SING N N 10 R1T "N4'" "H4'1" SING N N 11 R1T "N4'" "H4'2" SING N N 12 R1T "C5'" "C7'" SING N N 13 R1T "C5'" "C6'" SING Y N 14 R1T "C6'" "H6'" SING N N 15 R1T "C7'" C3 SING N N 16 R1T "C7'" "H7'1" SING N N 17 R1T "C7'" "H7'2" SING N N 18 R1T C3 C2 DOUB Y N 19 R1T C3 C4 SING Y N 20 R1T C2 CP1 SING N N 21 R1T C2 S1 SING Y N 22 R1T S1 C5 SING Y N 23 R1T C5 C4 DOUB Y N 24 R1T C5 C6 SING N N 25 R1T C4 CM4 SING N N 26 R1T CM4 HM41 SING N N 27 R1T CM4 HM42 SING N N 28 R1T CM4 HM43 SING N N 29 R1T C6 H61 SING N N 30 R1T C6 H62 SING N N 31 R1T C6 C7 SING N N 32 R1T C7 H71 SING N N 33 R1T C7 H72 SING N N 34 R1T C7 O7 SING N N 35 R1T O7 PA SING N N 36 R1T PA O1A DOUB N N 37 R1T PA O2A SING N N 38 R1T PA O3A SING N N 39 R1T O2A H2A SING N N 40 R1T O3A PB SING N N 41 R1T PB O1B DOUB N N 42 R1T PB O2B SING N N 43 R1T PB O3B SING N N 44 R1T O2B H2B SING N N 45 R1T O3B H3B SING N N 46 R1T CP1 OP1 SING N N 47 R1T CP1 H1 SING N N 48 R1T CP1 CP2 SING N N 49 R1T CP2 HP21 SING N N 50 R1T CP2 HP22 SING N N 51 R1T CP2 HP23 SING N N 52 R1T OP1 HP1 SING N N 53 # # 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 R1T SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)OCCc1sc(c(c1C)Cc2cnc(nc2N)C)C(O)C" R1T SMILES_CANONICAL CACTVS 3.341 "C[C@@H](O)c1sc(CCO[P@@](O)(=O)O[P](O)(O)=O)c(C)c1Cc2cnc(C)nc2N" R1T SMILES CACTVS 3.341 "C[CH](O)c1sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)c1Cc2cnc(C)nc2N" R1T SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "Cc1c(sc(c1Cc2cnc(nc2N)C)[C@@H](C)O)CCO[P@](=O)(O)OP(=O)(O)O" R1T SMILES "OpenEye OEToolkits" 1.5.0 "Cc1c(sc(c1Cc2cnc(nc2N)C)C(C)O)CCOP(=O)(O)OP(=O)(O)O" R1T InChI InChI 1.03 "InChI=1S/C15H23N3O8P2S/c1-8-12(6-11-7-17-10(3)18-15(11)16)14(9(2)19)29-13(8)4-5-25-28(23,24)26-27(20,21)22/h7,9,19H,4-6H2,1-3H3,(H,23,24)(H2,16,17,18)(H2,20,21,22)/t9-/m1/s1" R1T InChIKey InChI 1.03 ORVRYSKZCUVOLA-SECBINFHSA-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 R1T "SYSTEMATIC NAME" ACDLabs 10.04 "2-{4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-[(1R)-1-hydroxyethyl]-3-methylthiophen-2-yl}ethyl trihydrogen diphosphate" R1T "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "2-[4-[(4-amino-2-methyl-pyrimidin-5-yl)methyl]-5-(1-hydroxyethyl)-3-methyl-thiophen-2-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 R1T "Create component" 2007-06-18 RCSB R1T "Modify descriptor" 2011-06-04 RCSB R1T "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id R1T _pdbx_chem_comp_synonyms.name "2-[(1R)-1-HYDROXYETHYL]-3-DEAZA-THDP" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##