data_PRT # _chem_comp.id PRT _chem_comp.name " PHOSPHORIBOSYL ATP " _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H25 N5 O20 P4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "[[(2~{R},3~{S},4~{R},5~{R})-5-[6-azanylidene-1-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2003-08-15 _chem_comp.pdbx_modified_date 2021-03-13 _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 719.276 _chem_comp.one_letter_code ? _chem_comp.three_letter_code PRT _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 5UBG _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 PRT O1G O1 O 0 1 N N N 11.425 -22.638 -21.914 9.466 2.979 -1.893 O1G PRT 1 PRT PG P1 P 0 1 N N N 12.006 -22.004 -23.359 9.486 2.895 -0.285 PG PRT 2 PRT O2G O2 O 0 1 N N N 11.769 -23.013 -24.561 10.803 2.393 0.166 O2G PRT 3 PRT O3G O3 O 0 1 N N N 11.500 -20.651 -23.684 9.229 4.360 0.332 O3G PRT 4 PRT O3B O4 O 0 1 N N N 13.627 -22.025 -23.241 8.330 1.892 0.214 O3B PRT 5 PRT PB P2 P 0 1 N N N 14.674 -20.987 -23.901 8.206 0.290 0.315 PB PRT 6 PRT O1B O5 O 0 1 N N N 15.210 -21.527 -25.316 8.819 -0.329 -0.881 O1B PRT 7 PRT O2B O6 O 0 1 N N N 14.427 -19.537 -23.913 8.968 -0.225 1.636 O2B PRT 8 PRT O3A O7 O 0 1 N N N 15.738 -21.140 -22.749 6.652 -0.124 0.396 O3A PRT 9 PRT PA P3 P 0 1 N N N 17.060 -21.896 -22.788 5.852 -1.509 0.208 PA PRT 10 PRT O1A O8 O 0 1 N N N 16.748 -23.345 -22.308 5.775 -1.875 -1.358 O1A PRT 11 PRT O2A O9 O 0 1 N N N 17.848 -21.845 -24.049 6.558 -2.589 0.933 O2A PRT 12 PRT "O5'" O10 O 0 1 N N N 17.814 -21.214 -21.522 4.362 -1.352 0.797 "O5'" PRT 13 PRT "C5'" C1 C 0 1 N N N 17.213 -21.159 -20.234 3.437 -2.438 0.872 "C5'" PRT 14 PRT "C4'" C2 C 0 1 N N R 18.111 -20.289 -19.359 2.121 -1.946 1.479 "C4'" PRT 15 PRT "O4'" O11 O 0 1 N N N 19.391 -20.954 -19.159 1.489 -1.015 0.585 "O4'" PRT 16 PRT "C3'" C3 C 0 1 N N S 18.520 -18.943 -19.937 1.154 -3.132 1.664 "C3'" PRT 17 PRT "O3'" O12 O 0 1 N N N 17.493 -18.005 -19.763 0.806 -3.283 3.042 "O3'" PRT 18 PRT "C2'" C4 C 0 1 N N R 19.722 -18.630 -19.011 -0.090 -2.740 0.830 "C2'" PRT 19 PRT "O2'" O13 O 0 1 N N N 19.257 -18.124 -17.769 -1.294 -3.084 1.519 "O2'" PRT 20 PRT "C1'" C5 C 0 1 N N R 20.370 -19.970 -18.810 0.064 -1.202 0.720 "C1'" PRT 21 PRT N9 N1 N 0 1 Y N N 21.572 -20.211 -19.705 -0.637 -0.697 -0.463 N9 PRT 22 PRT C8 C6 C 0 1 Y N N 22.782 -20.543 -19.241 -0.107 -0.544 -1.714 C8 PRT 23 PRT C4 C7 C 0 1 Y N N 21.674 -20.137 -21.021 -1.933 -0.301 -0.520 C4 PRT 24 PRT C5 C8 C 0 1 Y N N 22.940 -20.424 -21.389 -2.156 0.098 -1.851 C5 PRT 25 PRT N7 N2 N 0 1 Y N N 23.618 -20.682 -20.273 -1.017 -0.067 -2.524 N7 PRT 26 PRT C6 C9 C 0 1 N N N 23.292 -20.414 -22.693 -3.492 0.596 -2.225 C6 PRT 27 PRT N6 N3 N 0 1 N N N 24.559 -20.702 -22.991 -3.729 1.301 -3.306 N6 PRT 28 PRT N3 N4 N 0 1 N N N 20.744 -19.847 -21.939 -2.918 -0.230 0.393 N3 PRT 29 PRT C2 C10 C 0 1 N N N 21.072 -19.828 -23.264 -4.133 0.065 0.002 C2 PRT 30 PRT N1 N5 N 0 1 N N N 22.381 -20.113 -23.649 -4.480 0.235 -1.305 N1 PRT 31 PRT C11 C11 C 0 1 N N R 22.633 -20.143 -25.107 -5.867 0.043 -1.738 C11 PRT 32 PRT C12 C12 C 0 1 N N R 23.617 -19.226 -25.719 -6.313 -1.423 -1.505 C12 PRT 33 PRT O12 O14 O 0 1 N N N 22.930 -18.021 -26.063 -5.955 -2.248 -2.615 O12 PRT 34 PRT C13 C13 C 0 1 N N S 23.934 -20.013 -26.988 -7.851 -1.280 -1.395 C13 PRT 35 PRT O13 O15 O 0 1 N N N 22.880 -19.856 -27.954 -8.475 -1.589 -2.642 O13 PRT 36 PRT O14 O16 O 0 1 N N N 23.184 -21.484 -25.304 -6.768 0.809 -0.911 O14 PRT 37 PRT C14 C14 C 0 1 N N R 23.913 -21.465 -26.548 -8.067 0.203 -1.036 C14 PRT 38 PRT C15 C15 C 0 1 N N N 25.317 -22.036 -26.312 -8.824 0.313 0.290 C15 PRT 39 PRT O15 O17 O 0 1 N N N 26.088 -21.152 -25.489 -9.122 1.685 0.556 O15 PRT 40 PRT P P4 P 0 1 N N N 27.692 -21.208 -25.543 -9.913 2.171 1.871 P PRT 41 PRT O3P O18 O 0 1 N N N 28.131 -22.450 -24.654 -10.185 3.755 1.779 O3P PRT 42 PRT O1P O19 O 0 1 N N N 28.129 -21.563 -27.024 -11.204 1.453 1.964 O1P PRT 43 PRT O2P O20 O 0 1 N N N 28.294 -19.984 -24.961 -9.028 1.854 3.178 O2P PRT 44 PRT H1 H1 H 0 1 N N N 11.053 -23.498 -22.072 8.631 3.301 -2.259 H1 PRT 45 PRT H2 H2 H 0 1 N N N 11.129 -20.653 -24.558 9.889 5.017 0.073 H2 PRT 46 PRT H3 H3 H 0 1 N N N 14.635 -19.187 -24.771 8.618 0.141 2.460 H3 PRT 47 PRT H4 H4 H 0 1 N N N 17.124 -23.969 -22.918 5.324 -1.210 -1.896 H4 PRT 48 PRT H5 H5 H 0 1 N N N 16.209 -20.715 -20.304 3.252 -2.829 -0.128 H5 PRT 49 PRT H6 H6 H 0 1 N N N 17.137 -22.171 -19.809 3.853 -3.227 1.499 H6 PRT 50 PRT H7 H7 H 0 1 N N N 17.617 -20.128 -18.389 2.312 -1.467 2.439 H7 PRT 51 PRT H8 H8 H 0 1 N N N 18.846 -19.040 -20.983 1.599 -4.050 1.281 H8 PRT 52 PRT H9 H9 H 0 1 N N N 17.761 -17.170 -20.128 0.199 -4.015 3.216 H9 PRT 53 PRT H10 H10 H 0 1 N N N 20.412 -17.933 -19.509 -0.061 -3.206 -0.155 H10 PRT 54 PRT H11 H11 H 0 1 N N N 19.999 -17.934 -17.206 -1.392 -4.031 1.692 H11 PRT 55 PRT H12 H12 H 0 1 N N N 20.671 -20.080 -17.758 -0.304 -0.714 1.622 H12 PRT 56 PRT H13 H13 H 0 1 N N N 23.041 -20.677 -18.201 0.910 -0.781 -1.991 H13 PRT 57 PRT H14 H14 H 0 1 N N N 25.102 -20.895 -22.173 -3.002 1.522 -3.910 H14 PRT 58 PRT H16 H16 H 0 1 N N N 20.324 -19.594 -24.007 -4.899 0.179 0.754 H16 PRT 59 PRT H17 H17 H 0 1 N N N 21.676 -20.058 -25.642 -5.981 0.317 -2.787 H17 PRT 60 PRT H18 H18 H 0 1 N N N 24.507 -19.068 -25.092 -5.892 -1.815 -0.579 H18 PRT 61 PRT H19 H19 H 0 1 N N N 22.733 -17.532 -25.273 -6.214 -3.175 -2.516 H19 PRT 62 PRT H20 H20 H 0 1 N N N 24.918 -19.733 -27.391 -8.236 -1.924 -0.604 H20 PRT 63 PRT H21 H21 H 0 1 N N N 22.859 -18.956 -28.257 -8.370 -2.510 -2.917 H21 PRT 64 PRT H22 H22 H 0 1 N N N 23.397 -22.071 -27.307 -8.632 0.697 -1.827 H22 PRT 65 PRT H23 H23 H 0 1 N N N 25.231 -23.012 -25.813 -9.752 -0.255 0.226 H23 PRT 66 PRT H24 H24 H 0 1 N N N 25.823 -22.163 -27.280 -8.207 -0.088 1.094 H24 PRT 67 PRT H25 H25 H 0 1 N N N 28.545 -23.104 -25.205 -10.660 4.118 2.540 H25 PRT 68 PRT H26 H26 H 0 1 N N N 28.876 -19.584 -25.596 -8.166 2.292 3.185 H26 PRT 69 # # 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 PRT O13 C13 SING N N 1 PRT O1P P DOUB N N 2 PRT C13 C14 SING N N 3 PRT C13 C12 SING N N 4 PRT C14 C15 SING N N 5 PRT C14 O14 SING N N 6 PRT C15 O15 SING N N 7 PRT O12 C12 SING N N 8 PRT C12 C11 SING N N 9 PRT P O15 SING N N 10 PRT P O2P SING N N 11 PRT P O3P SING N N 12 PRT O1B PB DOUB N N 13 PRT O14 C11 SING N N 14 PRT C11 N1 SING N N 15 PRT O2G PG DOUB N N 16 PRT O2A PA DOUB N N 17 PRT O2B PB SING N N 18 PRT PB O3B SING N N 19 PRT PB O3A SING N N 20 PRT O3G PG SING N N 21 PRT N1 C2 SING N N 22 PRT N1 C6 SING N N 23 PRT PG O3B SING N N 24 PRT PG O1G SING N N 25 PRT C2 N3 DOUB N N 26 PRT N6 C6 DOUB N N 27 PRT PA O3A SING N N 28 PRT PA O1A SING N N 29 PRT PA "O5'" SING N N 30 PRT C6 C5 SING N N 31 PRT N3 C4 SING N N 32 PRT "O5'" "C5'" SING N N 33 PRT C5 C4 DOUB Y N 34 PRT C5 N7 SING Y N 35 PRT C4 N9 SING Y N 36 PRT N7 C8 DOUB Y N 37 PRT "C5'" "C4'" SING N N 38 PRT "C3'" "O3'" SING N N 39 PRT "C3'" "C4'" SING N N 40 PRT "C3'" "C2'" SING N N 41 PRT N9 C8 SING Y N 42 PRT N9 "C1'" SING N N 43 PRT "C4'" "O4'" SING N N 44 PRT "O4'" "C1'" SING N N 45 PRT "C2'" "C1'" SING N N 46 PRT "C2'" "O2'" SING N N 47 PRT O1G H1 SING N N 48 PRT O3G H2 SING N N 49 PRT O2B H3 SING N N 50 PRT O1A H4 SING N N 51 PRT "C5'" H5 SING N N 52 PRT "C5'" H6 SING N N 53 PRT "C4'" H7 SING N N 54 PRT "C3'" H8 SING N N 55 PRT "O3'" H9 SING N N 56 PRT "C2'" H10 SING N N 57 PRT "O2'" H11 SING N N 58 PRT "C1'" H12 SING N N 59 PRT C8 H13 SING N N 60 PRT N6 H14 SING N N 61 PRT C2 H16 SING N N 62 PRT C11 H17 SING N N 63 PRT C12 H18 SING N N 64 PRT O12 H19 SING N N 65 PRT C13 H20 SING N N 66 PRT O13 H21 SING N N 67 PRT C14 H22 SING N N 68 PRT C15 H23 SING N N 69 PRT C15 H24 SING N N 70 PRT O3P H25 SING N N 71 PRT O2P H26 SING N N 72 # # 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 PRT InChI InChI 1.03 "InChI=1S/C15H25N5O20P4/c16-12-7-13(18-4-19(12)14-10(23)8(21)5(37-14)1-35-41(25,26)27)20(3-17-7)15-11(24)9(22)6(38-15)2-36-43(31,32)40-44(33,34)39-42(28,29)30/h3-6,8-11,14-16,21-24H,1-2H2,(H,31,32)(H,33,34)(H2,25,26,27)(H2,28,29,30)/b16-12-/t5-,6-,8-,9-,10-,11-,14-,15-/m1/s1" PRT InChIKey InChI 1.03 RKNHJBVBFHDXGR-DNVSJNHSSA-N PRT SMILES_CANONICAL CACTVS 3.385 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=Nc3n(cnc3C2=N)[C@@H]4O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]4O" PRT SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=Nc3n(cnc3C2=N)[CH]4O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]4O" PRT SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "[H]/N=C\1/c2c(n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=CN1[C@H]4[C@@H]([C@@H]([C@H](O4)COP(=O)(O)O)O)O" PRT SMILES "OpenEye OEToolkits" 2.0.6 "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=CN(C2=N)C4C(C(C(O4)COP(=O)(O)O)O)O" # _pdbx_chem_comp_identifier.comp_id PRT _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.6 _pdbx_chem_comp_identifier.identifier "[[(2~{R},3~{S},4~{R},5~{R})-5-[6-azanylidene-1-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] 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 PRT "Create component" 2003-08-15 RCSB PRT "Modify descriptor" 2011-06-04 RCSB PRT "Modify name" 2011-06-07 RCSB PRT "Modify descriptor" 2011-06-07 RCSB PRT "Modify identifier" 2011-06-07 RCSB PRT "Other modification" 2017-03-31 RCSB PRT "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id PRT _pdbx_chem_comp_synonyms.name "[[(2~{R},3~{S},4~{R},5~{R})-5-[6-azanylidene-1-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##