data_PAX # _chem_comp.id PAX _chem_comp.name ;5'-PHOSPHOTHYMIDINE (3'-5')-PYROPHOSPHATE ADENOSINE 3'-PHOSPHATE ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H27 N7 O20 P4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge -2 _chem_comp.pdbx_initial_date 2004-07-22 _chem_comp.pdbx_modified_date 2011-06-04 _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 809.358 _chem_comp.one_letter_code ? _chem_comp.three_letter_code PAX _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details "OpenEye/OEToolkits V1.4.2" _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1U1B _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 PAX PA PA P 0 1 N N N -24.136 -18.730 -9.572 3.644 4.572 0.057 PA PAX 1 PAX O1A O1A O -1 1 N N N -25.550 -19.310 -9.536 2.895 3.257 0.062 O1A PAX 2 PAX O2A O2A O 0 1 N N N -23.710 -18.040 -10.873 5.064 4.651 -0.461 O2A PAX 3 PAX "O5'" O5* O 0 1 N N N -23.925 -17.704 -8.369 2.721 5.683 -0.711 "O5'" PAX 4 PAX PB PB P 0 1 N N N -22.779 -20.736 -7.959 4.294 4.655 2.944 PB PAX 5 PAX O1B O1B O -1 1 N N N -22.023 -19.881 -7.013 3.633 3.349 3.329 O1B PAX 6 PAX O2B O2B O 0 1 N N N -24.034 -21.383 -7.523 5.797 4.749 2.800 O2B PAX 7 PAX O3A O3A O 0 1 N N N -23.096 -19.879 -9.247 3.600 5.194 1.567 O3A PAX 8 PAX PG PG P 0 1 N N N -29.230 -15.857 -8.064 3.049 11.320 -2.671 PG PAX 9 PAX O1G O1G O 0 1 N N N -29.417 -15.806 -6.548 3.497 11.299 -4.225 O1G PAX 10 PAX O2G O2G O 0 1 N N N -30.184 -14.949 -8.831 4.443 11.552 -1.885 O2G PAX 11 PAX O3G O3G O 0 1 N N N -29.297 -17.307 -8.575 1.960 12.294 -2.331 O3G PAX 12 PAX N9A N9A N 0 1 Y N N -24.014 -13.430 -9.846 1.091 9.592 2.007 N9A PAX 13 PAX C4A C4A C 0 1 Y N N -23.062 -13.762 -10.795 0.325 10.326 2.869 C4A PAX 14 PAX N3A N3A N 0 1 Y N N -22.842 -14.983 -11.376 -0.902 10.823 2.651 N3A PAX 15 PAX C2A C2A C 0 1 Y N N -21.813 -14.942 -12.276 -1.339 11.496 3.738 C2A PAX 16 PAX N1A N1A N 0 1 Y N N -21.038 -13.862 -12.619 -0.710 11.698 4.921 N1A PAX 17 PAX C6A C6A C 0 1 Y N N -21.291 -12.649 -12.010 0.527 11.167 5.071 C6A PAX 18 PAX N6A N6A N 0 1 N N N -20.536 -11.606 -12.348 1.230 11.342 6.275 N6A PAX 19 PAX C5A C5A C 0 1 Y N N -22.353 -12.571 -11.047 1.088 10.450 4.019 C5A PAX 20 PAX N7A N7A N 0 1 Y N N -22.848 -11.533 -10.284 2.293 9.810 3.873 N7A PAX 21 PAX C8A C8A C 0 1 Y N N -23.821 -12.086 -9.596 2.263 9.307 2.657 C8A PAX 22 PAX "C5'" C5* C 0 1 N N N -24.982 -17.399 -7.471 3.205 7.008 -0.849 "C5'" PAX 23 PAX "C4'" C4* C 0 1 N N R -25.551 -16.033 -7.756 2.027 7.965 -0.873 "C4'" PAX 24 PAX "O4'" O4* O 0 1 N N N -24.500 -15.104 -8.197 1.311 7.887 0.370 "O4'" PAX 25 PAX "C1'" C1* C 0 1 N N R -25.062 -14.247 -9.173 0.736 9.182 0.647 "C1'" PAX 26 PAX "C2'" C2* C 0 1 N N R -25.924 -15.230 -9.986 1.230 10.147 -0.433 "C2'" PAX 27 PAX "O2'" O2* O 0 1 N N N -26.795 -14.589 -10.916 0.210 10.314 -1.416 "O2'" PAX 28 PAX "C3'" C3* C 0 1 N N S -26.630 -16.001 -8.863 2.433 9.423 -1.007 "C3'" PAX 29 PAX "O3'" O3* O 0 1 N N N -27.738 -15.238 -8.359 2.716 9.775 -2.345 "O3'" PAX 30 PAX O5 O5 O 0 1 N N N -19.696 -22.514 -12.320 1.352 6.892 5.386 O5 PAX 31 PAX C5 C5 C 0 1 N N N -20.977 -23.003 -11.865 2.158 6.934 6.552 C5 PAX 32 PAX C4 C4 C 0 1 N N R -20.989 -23.121 -10.352 3.619 6.922 6.139 C4 PAX 33 PAX O4 O4 O 0 1 N N N -19.786 -23.773 -9.903 4.451 6.935 7.312 O4 PAX 34 PAX C1 C1 C 0 1 N N R -19.121 -22.977 -8.945 5.558 6.046 7.100 C1 PAX 35 PAX C2 C2 C 0 1 N N N -19.608 -21.559 -9.155 5.496 5.601 5.650 C2 PAX 36 PAX C3 C3 C 0 1 N N S -21.040 -21.791 -9.614 4.015 5.681 5.355 C3 PAX 37 PAX O3 O3 O 0 1 N N N -21.885 -21.950 -8.497 3.772 5.820 3.971 O3 PAX 38 PAX PD PD P 0 1 N N N -19.538 -21.643 -13.700 -0.257 6.895 5.560 PD PAX 39 PAX O1D O1D O 0 1 N N N -19.675 -22.675 -14.832 -0.513 5.648 6.558 O1D PAX 40 PAX O2D O2D O 0 1 N N N -18.134 -20.992 -13.636 -0.540 8.184 6.494 O2D PAX 41 PAX O3D O3D O 0 1 N N N -20.680 -20.612 -13.688 -1.034 6.849 4.277 O3D PAX 42 PAX N1T N1T N 0 1 Y N N -17.662 -23.150 -9.151 5.433 4.942 8.013 N1T PAX 43 PAX C6T C6T C 0 1 Y N N -17.075 -23.076 -10.441 4.329 4.901 8.856 C6T PAX 44 PAX C2T C2T C 0 1 Y N N -16.875 -23.396 -8.006 6.403 3.918 8.059 C2T PAX 45 PAX O2T O2T O 0 1 N N N -17.326 -23.463 -6.881 7.406 3.890 7.343 O2T PAX 46 PAX N3T N3T N 0 1 Y N N -15.522 -23.559 -8.269 6.154 2.907 8.994 N3T PAX 47 PAX C4T C4T C 0 1 Y N N -14.885 -23.499 -9.516 5.072 2.818 9.857 C4T PAX 48 PAX O4T O4T O 0 1 N N N -13.671 -23.670 -9.558 4.915 1.900 10.657 O4T PAX 49 PAX C5T C5T C 0 1 Y N N -15.753 -23.233 -10.656 4.094 3.933 9.749 C5T PAX 50 PAX CM5 CM5 C 0 1 N N N -15.196 -23.139 -12.044 2.898 3.908 10.647 CM5 PAX 51 PAX H1G H1G H 0 1 N N N -28.822 -16.372 -6.069 3.692 12.149 -4.674 H1G PAX 52 PAX H2A H2A H 0 1 N N N -21.580 -15.892 -12.785 -2.328 11.933 3.653 H2A PAX 53 PAX H6A1 1H6A H 0 0 N N N -20.722 -10.709 -11.898 2.157 11.723 6.254 H6A1 PAX 54 PAX H6A2 2H6A H 0 0 N N N -20.570 -11.484 -13.360 0.836 10.998 7.130 H6A2 PAX 55 PAX H8A H8A H 0 1 N N N -24.412 -11.485 -8.884 3.053 8.731 2.195 H8A PAX 56 PAX "H5'1" 1H5* H 0 0 N N N -25.772 -18.185 -7.482 3.864 7.232 -0.005 "H5'1" PAX 57 PAX "H5'2" 2H5* H 0 0 N N N -24.661 -17.498 -6.407 3.777 7.079 -1.779 "H5'2" PAX 58 PAX "H4'" H4* H 0 1 N N N -26.013 -15.735 -6.786 1.348 7.666 -1.681 "H4'" PAX 59 PAX "H1'" H1* H 0 1 N N N -25.712 -13.411 -8.824 -0.354 9.080 0.653 "H1'" PAX 60 PAX "H2'" H2* H 0 1 N N N -25.346 -15.891 -10.673 1.478 11.144 -0.059 "H2'" PAX 61 PAX H2 H2 H 0 1 N N N -27.326 -15.195 -11.417 0.652 10.512 -2.260 H2 PAX 62 PAX "H3'" H3* H 0 1 N N N -27.010 -16.996 -9.192 3.315 9.629 -0.389 "H3'" PAX 63 PAX H51 1H5 H 0 1 N N N -21.818 -22.375 -12.239 1.928 7.844 7.110 H51 PAX 64 PAX H52 2H5 H 0 1 N N N -21.254 -23.963 -12.359 1.932 6.063 7.172 H52 PAX 65 PAX H4 H4 H 0 1 N N N -21.917 -23.693 -10.122 3.829 7.834 5.568 H4 PAX 66 PAX H1 H1 H 0 1 N N N -19.332 -23.260 -7.887 6.493 6.561 7.337 H1 PAX 67 PAX H21 1H2 H 0 1 N N N -19.495 -20.883 -8.275 5.917 4.608 5.466 H21 PAX 68 PAX H22 2H2 H 0 1 N N N -18.984 -20.939 -9.840 6.040 6.308 5.011 H22 PAX 69 PAX H3 H3 H 0 1 N N N -21.420 -20.944 -10.232 3.499 4.787 5.724 H3 PAX 70 PAX H2D H2D H 0 1 N N N -18.042 -20.487 -14.435 -1.468 8.436 6.687 H2D PAX 71 PAX H6T H6T H 0 1 N N N -17.688 -22.883 -11.337 3.640 5.733 8.745 H6T PAX 72 PAX H3T H3T H 0 1 N N N -14.931 -23.742 -7.457 6.840 2.159 9.045 H3T PAX 73 PAX HM51 1HM5 H 0 0 N N N -14.102 -23.268 -12.221 2.313 3.010 10.456 HM51 PAX 74 PAX HM52 2HM5 H 0 0 N N N -15.744 -23.861 -12.691 2.281 4.787 10.462 HM52 PAX 75 PAX HM53 3HM5 H 0 0 N N N -15.508 -22.162 -12.481 3.220 3.916 11.688 HM53 PAX 76 PAX HO1 HO1 H 0 1 N N N -30.944 -14.760 -8.293 4.822 12.456 -1.848 HO1 PAX 77 PAX HO2 HO2 H 0 1 N N N -19.703 -22.226 -15.669 -1.436 5.378 6.752 HO2 PAX 78 # 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 PAX PA O1A SING N N 1 PAX PA O2A DOUB N N 2 PAX PA "O5'" SING N N 3 PAX PA O3A SING N N 4 PAX "O5'" "C5'" SING N N 5 PAX PB O1B SING N N 6 PAX PB O2B DOUB N N 7 PAX PB O3A SING N N 8 PAX PB O3 SING N N 9 PAX PG O1G SING N N 10 PAX PG O2G SING N N 11 PAX PG O3G DOUB N N 12 PAX PG "O3'" SING N N 13 PAX O1G H1G SING N N 14 PAX N9A C4A SING Y N 15 PAX N9A C8A SING Y N 16 PAX N9A "C1'" SING N N 17 PAX C4A N3A DOUB Y N 18 PAX C4A C5A SING Y N 19 PAX N3A C2A SING Y N 20 PAX C2A N1A DOUB Y N 21 PAX C2A H2A SING N N 22 PAX N1A C6A SING Y N 23 PAX C6A N6A SING N N 24 PAX C6A C5A DOUB Y N 25 PAX N6A H6A1 SING N N 26 PAX N6A H6A2 SING N N 27 PAX C5A N7A SING Y N 28 PAX N7A C8A DOUB Y N 29 PAX C8A H8A SING N N 30 PAX "C5'" "C4'" SING N N 31 PAX "C5'" "H5'1" SING N N 32 PAX "C5'" "H5'2" SING N N 33 PAX "C4'" "O4'" SING N N 34 PAX "C4'" "C3'" SING N N 35 PAX "C4'" "H4'" SING N N 36 PAX "O4'" "C1'" SING N N 37 PAX "C1'" "C2'" SING N N 38 PAX "C1'" "H1'" SING N N 39 PAX "C2'" "O2'" SING N N 40 PAX "C2'" "C3'" SING N N 41 PAX "C2'" "H2'" SING N N 42 PAX "O2'" H2 SING N N 43 PAX "C3'" "O3'" SING N N 44 PAX "C3'" "H3'" SING N N 45 PAX O5 C5 SING N N 46 PAX O5 PD SING N N 47 PAX C5 C4 SING N N 48 PAX C5 H51 SING N N 49 PAX C5 H52 SING N N 50 PAX C4 O4 SING N N 51 PAX C4 C3 SING N N 52 PAX C4 H4 SING N N 53 PAX O4 C1 SING N N 54 PAX C1 C2 SING N N 55 PAX C1 N1T SING N N 56 PAX C1 H1 SING N N 57 PAX C2 C3 SING N N 58 PAX C2 H21 SING N N 59 PAX C2 H22 SING N N 60 PAX C3 O3 SING N N 61 PAX C3 H3 SING N N 62 PAX PD O1D SING N N 63 PAX PD O2D SING N N 64 PAX PD O3D DOUB N N 65 PAX O2D H2D SING N N 66 PAX N1T C6T SING Y N 67 PAX N1T C2T SING Y N 68 PAX C6T C5T DOUB Y N 69 PAX C6T H6T SING N N 70 PAX C2T O2T DOUB N N 71 PAX C2T N3T SING Y N 72 PAX N3T C4T SING Y N 73 PAX N3T H3T SING N N 74 PAX C4T O4T DOUB N N 75 PAX C4T C5T SING Y N 76 PAX C5T CM5 SING N N 77 PAX CM5 HM51 SING N N 78 PAX CM5 HM52 SING N N 79 PAX CM5 HM53 SING N N 80 PAX HO1 O2G SING N N 81 PAX HO2 O1D SING N N 82 # 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 PAX SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@H]2C[C@H](O[P]([O-])(=O)O[P]([O-])(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O[P](O)(O)=O)n4cnc5c(N)ncnc45)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O" PAX SMILES CACTVS 3.341 "CC1=CN([CH]2C[CH](O[P]([O-])(=O)O[P]([O-])(=O)OC[CH]3O[CH]([CH](O)[CH]3O[P](O)(O)=O)n4cnc5c(N)ncnc45)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O" PAX SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O[P@@](=O)([O-])O[P@@](=O)([O-])OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)OP(=O)(O)O" PAX SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)OP(=O)([O-])OP(=O)([O-])OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)OP(=O)(O)O" PAX InChI InChI 1.03 ;InChI=1S/C20H29N7O20P4/c1-8-3-26(20(30)25-18(8)29)12-2-9(10(43-12)4-41-48(31,32)33)45-51(39,40)47-50(37,38)42-5-11-15(46-49(34,35)36)14(28)19(44-11)27-7-24-13-16(21)22-6-23-17(13)27/h3,6-7,9-12,14-15,19,28H,2,4-5H2,1H3,(H,37,38)(H,39,40)(H2,21,22,23)(H,25,29,30)(H2,31,32,33)(H2,34,35,36)/p-2/t9-,10+,11+,12+,14+,15+,19+/m0/s1 ; PAX InChIKey InChI 1.03 DQGQNMNTNSHMMC-SLFMBYJQSA-L # 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 PAX "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxy-oxolan-2-yl]methyl [[(2R,3S,5R)-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-2-(phosphonooxymethyl)oxolan-3-yl]oxy-oxido-phosphoryl] 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 PAX "Create component" 2004-07-22 RCSB PAX "Modify descriptor" 2011-06-04 RCSB #