data_YHZ # _chem_comp.id YHZ _chem_comp.name "1-[(4-aminopyrimidin-5-yl)amino]-2,5-anhydro-1-deoxy-6-O-[(S)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]oxy}phosphoryl]-D-allitol" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C11 H21 N4 O12 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-02-03 _chem_comp.pdbx_modified_date 2023-06-09 _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 494.225 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YHZ _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 8FXI _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 YHZ PG P1 P 0 1 N N N 191.063 170.793 125.290 5.943 -1.887 -0.544 PG YHZ 1 YHZ O1G O1 O 0 1 N N N 190.026 170.505 124.241 5.707 -2.647 0.704 O1G YHZ 2 YHZ O2G O2 O 0 1 N N N 190.600 170.408 126.666 7.116 -0.812 -0.303 O2G YHZ 3 YHZ O3G O3 O 0 1 N N N 192.398 170.190 124.946 6.377 -2.902 -1.716 O3G YHZ 4 YHZ PB P2 P 0 1 N N N 191.120 173.282 123.636 3.922 0.128 0.302 PB YHZ 5 YHZ O1B O4 O 0 1 N N N 191.802 172.348 122.676 3.686 -0.632 1.550 O1B YHZ 6 YHZ O2B O5 O 0 1 N N N 189.659 173.532 123.391 5.095 1.204 0.543 O2B YHZ 7 YHZ C3B C1 C 0 1 N N N 191.293 172.569 125.295 4.413 -1.020 -1.025 C3B YHZ 8 YHZ PA P3 P 0 1 N N N 192.628 175.462 124.856 1.645 2.005 0.584 PA YHZ 9 YHZ O1A O6 O 0 1 N N N 193.061 176.783 124.312 1.526 1.702 2.028 O1A YHZ 10 YHZ O2A O7 O 0 1 N N N 191.728 175.456 126.045 2.310 3.458 0.393 O2A YHZ 11 YHZ O3A O8 O 0 1 N N N 191.917 174.652 123.673 2.571 0.894 -0.123 O3A YHZ 12 YHZ "O5'" O9 O 0 1 N N N 193.919 174.554 125.156 0.182 1.992 -0.089 "O5'" YHZ 13 YHZ "C5'" C2 C 0 1 N N N 194.453 173.662 124.141 -0.901 2.792 0.389 "C5'" YHZ 14 YHZ "C4'" C3 C 0 1 N N R 195.940 173.476 124.338 -2.140 2.539 -0.473 "C4'" YHZ 15 YHZ "O4'" O10 O 0 1 N N N 196.649 174.463 123.548 -2.653 1.210 -0.238 "O4'" YHZ 16 YHZ "C3'" C4 C 0 1 N N S 196.475 173.646 125.764 -3.288 3.485 -0.055 "C3'" YHZ 17 YHZ "O3'" O11 O 0 1 N N N 196.490 172.397 126.443 -3.353 4.611 -0.932 "O3'" YHZ 18 YHZ "C2'" C5 C 0 1 N N R 197.898 174.159 125.538 -4.559 2.617 -0.192 "C2'" YHZ 19 YHZ "O2'" O12 O 0 1 N N N 198.822 173.105 125.380 -5.449 3.182 -1.156 "O2'" YHZ 20 YHZ "C1'" C6 C 0 1 N N S 197.747 174.983 124.263 -4.028 1.249 -0.677 "C1'" YHZ 21 YHZ C8 C7 C 0 1 N N N 196.273 176.990 124.671 -4.825 0.111 -0.036 C8 YHZ 22 YHZ N7 N1 N 0 1 N N N 196.344 178.276 124.900 -4.259 -1.175 -0.450 N7 YHZ 23 YHZ C5 C8 C 0 1 Y N N 197.704 178.547 124.905 -4.824 -2.370 0.012 C5 YHZ 24 YHZ C6 C9 C 0 1 Y N N 198.430 179.736 125.100 -4.297 -3.611 -0.371 C6 YHZ 25 YHZ N6 N2 N 0 1 N N N 197.867 180.916 125.333 -3.200 -3.681 -1.220 N6 YHZ 26 YHZ N1 N3 N 0 1 Y N N 199.779 179.661 125.041 -4.864 -4.720 0.091 N1 YHZ 27 YHZ C2 C10 C 0 1 Y N N 200.340 178.470 124.808 -5.905 -4.659 0.897 C2 YHZ 28 YHZ N3 N4 N 0 1 Y N N 199.761 177.290 124.613 -6.427 -3.510 1.277 N3 YHZ 29 YHZ C4 C11 C 0 1 Y N N 198.425 177.395 124.674 -5.916 -2.358 0.866 C4 YHZ 30 YHZ H1 H1 H 0 1 N N N 189.722 170.048 126.616 7.325 -0.276 -1.081 H1 YHZ 31 YHZ H2 H2 H 0 1 N N N 192.335 169.732 124.116 7.185 -3.398 -1.527 H2 YHZ 32 YHZ H3 H3 H 0 1 N N N 189.376 173.038 122.631 5.304 1.739 -0.235 H3 YHZ 33 YHZ H4 H4 H 0 1 N N N 192.300 172.796 125.676 4.587 -0.461 -1.944 H4 YHZ 34 YHZ H5 H5 H 0 1 N N N 190.540 173.023 125.957 3.619 -1.749 -1.188 H5 YHZ 35 YHZ H6 H6 H 0 1 N N N 191.544 176.350 126.308 2.419 3.723 -0.530 H6 YHZ 36 YHZ H7 H7 H 0 1 N N N 194.270 174.093 123.146 -1.118 2.529 1.424 H7 YHZ 37 YHZ H8 H8 H 0 1 N N N 193.952 172.686 124.216 -0.628 3.846 0.331 H8 YHZ 38 YHZ H9 H9 H 0 1 N N N 196.213 172.469 123.988 -1.902 2.675 -1.528 H9 YHZ 39 YHZ H10 H10 H 0 1 N N N 195.881 174.398 126.305 -3.157 3.812 0.977 H10 YHZ 40 YHZ H11 H11 H 0 1 N N N 196.824 172.519 127.324 -4.057 5.238 -0.715 H11 YHZ 41 YHZ H12 H12 H 0 1 N N N 198.186 174.819 126.370 -5.057 2.513 0.772 H12 YHZ 42 YHZ H13 H13 H 0 1 N N N 198.888 172.617 126.192 -5.765 4.067 -0.928 H13 YHZ 43 YHZ H14 H14 H 0 1 N N N 198.651 175.345 123.751 -4.081 1.185 -1.764 H14 YHZ 44 YHZ H15 H15 H 0 1 N N N 195.692 176.652 125.542 -4.775 0.198 1.049 H15 YHZ 45 YHZ H16 H16 H 0 1 N N N 195.636 176.970 123.775 -5.865 0.170 -0.358 H16 YHZ 46 YHZ H17 H17 H 0 1 N N N 195.883 178.791 124.177 -3.492 -1.199 -1.044 H17 YHZ 47 YHZ H18 H18 H 0 1 N N N 198.579 181.611 125.435 -2.792 -2.866 -1.552 H18 YHZ 48 YHZ H19 H19 H 0 1 N N N 197.272 181.158 124.567 -2.842 -4.544 -1.480 H19 YHZ 49 YHZ H20 H20 H 0 1 N N N 201.419 178.466 124.773 -6.345 -5.578 1.256 H20 YHZ 50 YHZ H21 H21 H 0 1 N N N 197.858 176.487 124.528 -6.351 -1.422 1.185 H21 YHZ 51 # 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 YHZ O1B PB DOUB N N 1 YHZ O2B PB SING N N 2 YHZ "O4'" "C1'" SING N N 3 YHZ "O4'" "C4'" SING N N 4 YHZ PB O3A SING N N 5 YHZ PB C3B SING N N 6 YHZ O3A PA SING N N 7 YHZ "C5'" "C4'" SING N N 8 YHZ "C5'" "O5'" SING N N 9 YHZ O1G PG DOUB N N 10 YHZ "C1'" "C2'" SING N N 11 YHZ O1A PA DOUB N N 12 YHZ "C4'" "C3'" SING N N 13 YHZ N3 C4 DOUB Y N 14 YHZ N3 C2 SING Y N 15 YHZ C8 N7 SING N N 16 YHZ C4 C5 SING Y N 17 YHZ C2 N1 DOUB Y N 18 YHZ PA "O5'" SING N N 19 YHZ PA O2A SING N N 20 YHZ N7 C5 SING N N 21 YHZ C5 C6 DOUB Y N 22 YHZ O3G PG SING N N 23 YHZ N1 C6 SING Y N 24 YHZ C6 N6 SING N N 25 YHZ PG C3B SING N N 26 YHZ PG O2G SING N N 27 YHZ "O2'" "C2'" SING N N 28 YHZ "C2'" "C3'" SING N N 29 YHZ "C3'" "O3'" SING N N 30 YHZ "C1'" C8 SING N N 31 YHZ O2G H1 SING N N 32 YHZ O3G H2 SING N N 33 YHZ O2B H3 SING N N 34 YHZ C3B H4 SING N N 35 YHZ C3B H5 SING N N 36 YHZ O2A H6 SING N N 37 YHZ "C5'" H7 SING N N 38 YHZ "C5'" H8 SING N N 39 YHZ "C4'" H9 SING N N 40 YHZ "C3'" H10 SING N N 41 YHZ "O3'" H11 SING N N 42 YHZ "C2'" H12 SING N N 43 YHZ "O2'" H13 SING N N 44 YHZ "C1'" H14 SING N N 45 YHZ C8 H15 SING N N 46 YHZ C8 H16 SING N N 47 YHZ N7 H17 SING N N 48 YHZ N6 H18 SING N N 49 YHZ N6 H19 SING N N 50 YHZ C2 H20 SING N N 51 YHZ C4 H21 SING N N 52 # 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 YHZ SMILES ACDLabs 12.01 "O=P(O)(O)CP(=O)(O)OP(=O)(O)OCC1OC(CNc2cncnc2N)C(O)C1O" YHZ InChI InChI 1.06 "InChI=1S/C11H21N4O12P3/c12-11-6(1-13-4-15-11)14-2-7-9(16)10(17)8(26-7)3-25-30(23,24)27-29(21,22)5-28(18,19)20/h1,4,7-10,14,16-17H,2-3,5H2,(H,21,22)(H,23,24)(H2,12,13,15)(H2,18,19,20)/t7-,8+,9-,10+/m0/s1" YHZ InChIKey InChI 1.06 KVTJTUTWTFKEKT-QCLAVDOMSA-N YHZ SMILES_CANONICAL CACTVS 3.385 "Nc1ncncc1NC[C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]2O" YHZ SMILES CACTVS 3.385 "Nc1ncncc1NC[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]2O" YHZ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1c(c(ncn1)N)NC[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O)O" YHZ SMILES "OpenEye OEToolkits" 2.0.7 "c1c(c(ncn1)N)NCC2C(C(C(O2)COP(=O)(O)OP(=O)(CP(=O)(O)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 YHZ "SYSTEMATIC NAME" ACDLabs 12.01 "1-[(4-aminopyrimidin-5-yl)amino]-2,5-anhydro-1-deoxy-6-O-[(S)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]oxy}phosphoryl]-D-allitol" YHZ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[[[(2~{R},3~{S},4~{R},5~{S})-5-[[(4-azanylpyrimidin-5-yl)amino]methyl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-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 YHZ "Create component" 2023-02-03 RCSB YHZ "Initial release" 2023-06-14 RCSB #