data_TD6 # _chem_comp.id TD6 _chem_comp.name "(4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H25 N4 O10 P2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2013-02-08 _chem_comp.pdbx_modified_date 2013-11-08 _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 527.403 _chem_comp.one_letter_code ? _chem_comp.three_letter_code TD6 _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 3ZHS _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 TD6 S1 S1 S 0 1 Y N N -8.289 16.262 41.433 0.989 0.792 -1.545 S1 TD6 1 TD6 C2 C2 C 0 1 Y N N -9.153 15.275 40.464 2.383 0.564 -0.581 C2 TD6 2 TD6 N3 N3 N 1 1 Y N N -9.540 14.020 41.165 2.179 -0.373 0.283 N3 TD6 3 TD6 C4 C4 C 0 1 Y N N -9.125 14.099 42.492 0.997 -0.955 0.269 C4 TD6 4 TD6 C5 C5 C 0 1 Y N N -8.422 15.279 42.774 0.157 -0.483 -0.658 C5 TD6 5 TD6 C6 C6 C 0 1 N N N -7.955 15.687 44.145 -1.252 -0.958 -0.901 C6 TD6 6 TD6 C7 C7 C 0 1 N N N -6.445 15.651 44.155 -2.221 -0.142 -0.042 C7 TD6 7 TD6 O7 O7 O 0 1 N N N -5.893 15.823 45.489 -3.557 -0.592 -0.273 O7 TD6 8 TD6 PA PA P 0 1 N N N -4.268 15.857 45.568 -4.837 0.045 0.467 PA TD6 9 TD6 PB PB P 0 1 N N N -3.983 18.690 44.514 -7.730 -0.169 -0.143 PB TD6 10 TD6 "N1'" "N1'" N 0 1 Y N N -8.946 9.417 41.004 4.596 -3.270 -1.151 "N1'" TD6 11 TD6 C11 C11 C 0 1 N N S -9.714 15.735 39.092 3.665 1.344 -0.720 C11 TD6 12 TD6 C13 C13 C 0 1 N N N -11.625 17.303 39.901 4.809 3.495 -0.166 C13 TD6 13 TD6 O1A O1A O 0 1 N N N -3.525 14.629 45.218 -4.860 1.508 0.240 O1A TD6 14 TD6 O1B O1B O 0 1 N N N -4.263 19.135 45.925 -8.654 -1.458 -0.417 O1B TD6 15 TD6 "C2'" "C2'" C 0 1 Y N N -7.860 9.422 40.225 5.663 -3.690 -0.501 "C2'" TD6 16 TD6 O2A O2A O 0 1 N N N -4.011 16.386 46.981 -4.747 -0.252 2.046 O2A TD6 17 TD6 O2B O2B O 0 1 N N N -5.267 18.769 43.696 -8.087 0.424 1.165 O2B TD6 18 TD6 "N3'" "N3'" N 0 1 Y N N -7.449 10.446 39.470 5.985 -3.216 0.686 "N3'" TD6 19 TD6 O3A O3A O 0 1 N N N -3.966 17.159 44.796 -6.182 -0.611 -0.127 O3A TD6 20 TD6 O3B O3B O 0 1 N N N -2.716 19.252 43.925 -7.966 0.918 -1.307 O3B TD6 21 TD6 "C4'" "C4'" C 0 1 Y N N -8.185 11.573 39.484 5.235 -2.289 1.273 "C4'" TD6 22 TD6 "N4'" "N4'" N 0 1 N N N -7.801 12.551 38.669 5.577 -1.793 2.520 "N4'" TD6 23 TD6 "C5'" "C5'" C 0 1 Y N N -9.352 11.677 40.303 4.097 -1.822 0.611 "C5'" TD6 24 TD6 "C6'" "C6'" C 0 1 Y N N -9.664 10.547 41.021 3.799 -2.348 -0.630 "C6'" TD6 25 TD6 "C7'" "C7'" C 0 1 N N N -10.218 12.900 40.482 3.216 -0.772 1.237 "C7'" TD6 26 TD6 OL1 OL1 O 0 1 N N N -9.516 14.781 38.046 4.013 1.445 -2.103 OL1 TD6 27 TD6 OL2 OL2 O 0 1 N N N -10.061 19.022 39.291 5.664 5.718 0.484 OL2 TD6 28 TD6 OL3 OL3 O 0 1 N N N -12.165 19.147 38.572 3.533 5.225 0.798 OL3 TD6 29 TD6 CLB CLB C 0 1 N N N -11.212 16.028 39.166 3.475 2.746 -0.138 CLB TD6 30 TD6 CLC CLC C 0 1 N N N -11.195 18.572 39.226 4.621 4.876 0.407 CLC TD6 31 TD6 CM2 CM2 C 0 1 N N N -7.027 8.180 40.203 6.540 -4.740 -1.133 CM2 TD6 32 TD6 CM4 CM4 C 0 1 N N N -9.547 13.094 43.520 0.622 -2.062 1.221 CM4 TD6 33 TD6 H6 H6 H 0 1 N N N -8.305 16.705 44.371 -1.503 -0.828 -1.954 H6 TD6 34 TD6 H6A H6A H 0 1 N N N -8.350 14.988 44.897 -1.331 -2.012 -0.636 H6A TD6 35 TD6 H7 H7 H 0 1 N N N -6.113 14.680 43.758 -1.970 -0.272 1.011 H7 TD6 36 TD6 H7A H7A H 0 1 N N N -6.069 16.459 43.511 -2.142 0.912 -0.307 H7A TD6 37 TD6 H11 H11 H 0 1 N N N -9.203 16.671 38.824 4.462 0.832 -0.182 H11 TD6 38 TD6 H13 H13 H 0 1 N N N -12.722 17.312 39.985 5.543 2.951 0.428 H13 TD6 39 TD6 H13A H13A H 0 0 N N N -11.180 17.280 40.907 5.160 3.573 -1.195 H13A TD6 40 TD6 HO1B HO1B H 0 0 N N N -5.180 19.371 46.007 -9.601 -1.266 -0.440 HO1B TD6 41 TD6 HO2A HO2A H 0 0 N N N -3.391 15.819 47.424 -4.728 -1.192 2.270 HO2A TD6 42 TD6 HO3B HO3B H 0 0 N N N -2.897 19.606 43.062 -7.752 0.597 -2.194 HO3B TD6 43 TD6 "HN4'" "HN4'" H 0 0 N N N -6.989 12.263 38.161 6.416 -2.053 2.933 "HN4'" TD6 44 TD6 HN4A HN4A H 0 0 N N N -8.539 12.759 38.027 4.978 -1.186 2.982 HN4A TD6 45 TD6 "H6'" "H6'" H 0 1 N N N -10.548 10.572 41.641 2.927 -2.011 -1.171 "H6'" TD6 46 TD6 "H7'" "H7'" H 0 1 N N N -11.100 12.616 41.075 3.819 0.097 1.503 "H7'" TD6 47 TD6 "H7'A" "H7'A" H 0 0 N N N -10.540 13.245 39.488 2.748 -1.177 2.134 "H7'A" TD6 48 TD6 HOL1 HOL1 H 0 0 N N N -9.879 15.119 37.236 3.347 1.891 -2.644 HOL1 TD6 49 TD6 HOL2 HOL2 H 0 0 N N N -10.013 19.834 38.800 5.495 6.593 0.859 HOL2 TD6 50 TD6 HLB HLB H 0 1 N N N -11.589 16.100 38.135 2.740 3.290 -0.733 HLB TD6 51 TD6 HLBA HLBA H 0 0 N N N -11.693 15.179 39.674 3.124 2.668 0.891 HLBA TD6 52 TD6 HM2 HM2 H 0 1 N N N -7.473 7.427 40.870 7.312 -4.257 -1.732 HM2 TD6 53 TD6 HM2A HM2A H 0 0 N N N -6.987 7.784 39.178 7.008 -5.341 -0.353 HM2A TD6 54 TD6 HM2B HM2B H 0 0 N N N -6.009 8.416 40.545 5.934 -5.383 -1.772 HM2B TD6 55 TD6 HM4 HM4 H 0 1 N N N -8.786 12.303 43.594 0.189 -1.633 2.124 HM4 TD6 56 TD6 HM4A HM4A H 0 0 N N N -9.655 13.591 44.495 -0.106 -2.719 0.745 HM4A TD6 57 TD6 HM4B HM4B H 0 0 N N N -10.510 12.650 43.225 1.513 -2.634 1.481 HM4B TD6 58 # 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 TD6 C2 S1 SING Y N 1 TD6 S1 C5 SING Y N 2 TD6 C11 C2 SING N N 3 TD6 C2 N3 DOUB Y N 4 TD6 "C7'" N3 SING N N 5 TD6 N3 C4 SING Y N 6 TD6 C4 C5 DOUB Y N 7 TD6 C4 CM4 SING N N 8 TD6 C5 C6 SING N N 9 TD6 C6 C7 SING N N 10 TD6 C6 H6 SING N N 11 TD6 C6 H6A SING N N 12 TD6 C7 O7 SING N N 13 TD6 C7 H7 SING N N 14 TD6 C7 H7A SING N N 15 TD6 O7 PA SING N N 16 TD6 O3A PA SING N N 17 TD6 O1A PA DOUB N N 18 TD6 PA O2A SING N N 19 TD6 O2B PB DOUB N N 20 TD6 O3B PB SING N N 21 TD6 PB O3A SING N N 22 TD6 PB O1B SING N N 23 TD6 "C2'" "N1'" DOUB Y N 24 TD6 "N1'" "C6'" SING Y N 25 TD6 OL1 C11 SING N N 26 TD6 C11 CLB SING N N 27 TD6 C11 H11 SING N N 28 TD6 CLB C13 SING N N 29 TD6 CLC C13 SING N N 30 TD6 C13 H13 SING N N 31 TD6 C13 H13A SING N N 32 TD6 O1B HO1B SING N N 33 TD6 "N3'" "C2'" SING Y N 34 TD6 CM2 "C2'" SING N N 35 TD6 O2A HO2A SING N N 36 TD6 "N3'" "C4'" DOUB Y N 37 TD6 O3B HO3B SING N N 38 TD6 "N4'" "C4'" SING N N 39 TD6 "C4'" "C5'" SING Y N 40 TD6 "N4'" "HN4'" SING N N 41 TD6 "N4'" HN4A SING N N 42 TD6 "C5'" "C7'" SING N N 43 TD6 "C5'" "C6'" DOUB Y N 44 TD6 "C6'" "H6'" SING N N 45 TD6 "C7'" "H7'" SING N N 46 TD6 "C7'" "H7'A" SING N N 47 TD6 OL1 HOL1 SING N N 48 TD6 CLC OL2 SING N N 49 TD6 OL2 HOL2 SING N N 50 TD6 OL3 CLC DOUB N N 51 TD6 CLB HLB SING N N 52 TD6 CLB HLBA SING N N 53 TD6 CM2 HM2 SING N N 54 TD6 CM2 HM2A SING N N 55 TD6 CM2 HM2B SING N N 56 TD6 CM4 HM4 SING N N 57 TD6 CM4 HM4A SING N N 58 TD6 CM4 HM4B SING N N 59 # 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 TD6 SMILES ACDLabs 12.01 "O=C(O)CCC(O)c1sc(c(n1Cc2cnc(nc2N)C)C)CCOP(=O)(O)OP(=O)(O)O" TD6 InChI InChI 1.03 "InChI=1S/C16H26N4O10P2S/c1-9-13(5-6-29-32(27,28)30-31(24,25)26)33-16(12(21)3-4-14(22)23)20(9)8-11-7-18-10(2)19-15(11)17/h7,12,20-21H,3-6,8H2,1-2H3,(H,22,23)(H,27,28)(H2,17,18,19)(H2,24,25,26)/t12-/m0/s1" TD6 InChIKey InChI 1.03 RWCNVMPVYGBSHH-LBPRGKRZSA-N TD6 SMILES_CANONICAL CACTVS 3.370 "Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C@@H](O)CCC(O)=O)c(N)n1" TD6 SMILES CACTVS 3.370 "Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[CH](O)CCC(O)=O)c(N)n1" TD6 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@H](CCC(=O)O)O)CCOP(=O)(O)OP(=O)(O)O" TD6 SMILES "OpenEye OEToolkits" 1.7.6 "Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(CCC(=O)O)O)CCOP(=O)(O)OP(=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 TD6 "SYSTEMATIC NAME" ACDLabs 12.01 "(4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid" TD6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(4S)-4-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3-ium-2-yl]-4-oxidanyl-butanoic 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 TD6 "Create component" 2013-02-08 EBI TD6 "Initial release" 2013-11-13 RCSB #