data_PAP # _chem_comp.id PAP _chem_comp.name "3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H16 N5 O13 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _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 507.181 _chem_comp.one_letter_code ? _chem_comp.three_letter_code PAP _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1AFK _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 PAP PB PB P 0 1 N N N 9.258 6.812 2.645 -1.992 0.093 -5.676 PB PAP 1 PAP O1B O1B O 0 1 N N N 10.422 6.162 1.996 -2.266 -1.348 -5.484 O1B PAP 2 PAP O2B O2B O 0 1 N N N 8.945 6.260 4.012 -3.181 0.755 -6.536 O2B PAP 3 PAP O3B O3B O 0 1 N N N 8.067 7.007 1.764 -0.597 0.275 -6.459 O3B PAP 4 PAP PA PA P 0 1 N N R 10.289 9.766 3.240 -0.698 0.109 -3.438 PA PAP 5 PAP O1A O1A O 0 1 N N N 10.561 9.640 4.712 0.563 0.276 -4.192 O1A PAP 6 PAP O2A O2A O 0 1 N N N 9.823 11.130 2.790 -1.018 -1.459 -3.267 O2A PAP 7 PAP O3A O3A O 0 1 N N N 9.292 8.504 2.626 -1.901 0.817 -4.241 O3A PAP 8 PAP "O5'" O5* O 0 1 N N N 11.481 9.226 2.221 -0.549 0.787 -1.986 "O5'" PAP 9 PAP "C5'" C5* C 0 1 N N N 11.050 8.984 0.867 0.527 0.119 -1.326 "C5'" PAP 10 PAP "C4'" C4* C 0 1 N N R 11.886 9.754 -0.056 0.722 0.719 0.067 "C4'" PAP 11 PAP "O4'" O4* O 0 1 N N N 11.673 9.519 -1.454 -0.466 0.536 0.865 "O4'" PAP 12 PAP "C3'" C3* C 0 1 N N S 11.590 11.105 0.204 1.831 -0.037 0.830 "C3'" PAP 13 PAP "O3'" O3* O 0 1 N N N 12.911 11.729 -0.148 3.070 0.668 0.745 "O3'" PAP 14 PAP P P P 0 1 N N N 13.963 12.898 0.574 4.121 -0.320 0.030 P PAP 15 PAP O1 O1 O 0 1 N N N 14.966 13.216 -0.521 3.624 -0.675 -1.318 O1 PAP 16 PAP O2 O2 O 0 1 N N N 13.100 14.071 1.018 5.547 0.415 -0.099 O2 PAP 17 PAP O3 O3 O 0 1 N N N 14.472 12.027 1.692 4.285 -1.657 0.911 O3 PAP 18 PAP "C2'" C2* C 0 1 N N R 10.395 11.134 -0.807 1.325 -0.071 2.292 "C2'" PAP 19 PAP "O2'" O2* O 0 1 N N N 9.930 12.472 -0.479 2.238 0.610 3.154 "O2'" PAP 20 PAP "C1'" C1* C 0 1 N N R 11.404 10.789 -1.995 -0.029 0.667 2.235 "C1'" PAP 21 PAP N9 N9 N 0 1 Y N N 11.162 10.379 -3.457 -0.993 0.035 3.140 N9 PAP 22 PAP C8 C8 C 0 1 Y N N 12.127 10.402 -4.554 -1.830 -0.995 2.835 C8 PAP 23 PAP N7 N7 N 0 1 Y N N 11.736 9.929 -5.752 -2.550 -1.307 3.873 N7 PAP 24 PAP C5 C5 C 0 1 Y N N 10.380 9.561 -5.413 -2.216 -0.501 4.910 C5 PAP 25 PAP C6 C6 C 0 1 Y N N 9.352 8.956 -6.172 -2.652 -0.370 6.240 C6 PAP 26 PAP N6 N6 N 0 1 N N N 9.548 8.784 -7.418 -3.637 -1.200 6.747 N6 PAP 27 PAP N1 N1 N 0 1 Y N N 8.150 8.660 -5.608 -2.092 0.564 7.001 N1 PAP 28 PAP C2 C2 C 0 1 Y N N 7.987 8.988 -4.338 -1.152 1.360 6.525 C2 PAP 29 PAP N3 N3 N 0 1 Y N N 8.819 9.573 -3.446 -0.717 1.278 5.285 N3 PAP 30 PAP C4 C4 C 0 1 Y N N 10.034 9.831 -4.058 -1.218 0.373 4.450 C4 PAP 31 PAP HOB2 2HOB H 0 0 N N N 8.199 6.676 4.427 -3.202 0.294 -7.386 HOB2 PAP 32 PAP HOB3 3HOB H 0 0 N N N 7.321 7.423 2.179 -0.457 1.226 -6.563 HOB3 PAP 33 PAP HOA2 2HOA H 0 0 N N N 9.651 11.209 1.859 -1.846 -1.523 -2.772 HOA2 PAP 34 PAP "H5'1" 1H5* H 0 0 N N N 11.036 7.897 0.616 1.441 0.243 -1.907 "H5'1" PAP 35 PAP "H5'2" 2H5* H 0 0 N N N 9.963 9.193 0.726 0.295 -0.941 -1.235 "H5'2" PAP 36 PAP "H4'" H4* H 0 1 N N N 12.942 9.447 0.125 0.969 1.778 -0.008 "H4'" PAP 37 PAP "H3'" H3* H 0 1 N N N 11.294 11.581 1.167 1.941 -1.049 0.440 "H3'" PAP 38 PAP HO2 HO2 H 0 1 N N N 13.677 14.712 1.414 6.145 -0.209 -0.532 HO2 PAP 39 PAP HO3 HO3 H 0 1 N N N 15.049 12.668 2.088 4.609 -1.382 1.779 HO3 PAP 40 PAP "H2'" H2* H 0 1 N N N 9.459 10.537 -0.917 1.185 -1.100 2.624 "H2'" PAP 41 PAP "HO2'" *HO2 H 0 0 N N N 9.204 12.489 -1.092 1.873 0.557 4.047 "HO2'" PAP 42 PAP "H1'" H1* H 0 1 N N N 11.989 11.721 -2.169 0.099 1.718 2.493 "H1'" PAP 43 PAP H8 H8 H 0 1 N N N 13.160 10.780 -4.477 -1.888 -1.482 1.872 H8 PAP 44 PAP HN61 1HN6 H 0 0 N N N 8.806 8.347 -7.965 -3.926 -1.102 7.668 HN61 PAP 45 PAP HN62 2HN6 H 0 0 N N N 10.413 8.259 -7.550 -4.041 -1.876 6.181 HN62 PAP 46 PAP H2 H2 H 0 1 N N N 6.984 8.729 -3.957 -0.724 2.107 7.178 H2 PAP 47 # 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 PAP PB O1B DOUB N N 1 PAP PB O2B SING N N 2 PAP PB O3B SING N N 3 PAP PB O3A SING N N 4 PAP O2B HOB2 SING N N 5 PAP O3B HOB3 SING N N 6 PAP PA O1A DOUB N N 7 PAP PA O2A SING N N 8 PAP PA O3A SING N N 9 PAP PA "O5'" SING N N 10 PAP O2A HOA2 SING N N 11 PAP "O5'" "C5'" SING N N 12 PAP "C5'" "C4'" SING N N 13 PAP "C5'" "H5'1" SING N N 14 PAP "C5'" "H5'2" SING N N 15 PAP "C4'" "O4'" SING N N 16 PAP "C4'" "C3'" SING N N 17 PAP "C4'" "H4'" SING N N 18 PAP "O4'" "C1'" SING N N 19 PAP "C3'" "O3'" SING N N 20 PAP "C3'" "C2'" SING N N 21 PAP "C3'" "H3'" SING N N 22 PAP "O3'" P SING N N 23 PAP P O1 DOUB N N 24 PAP P O2 SING N N 25 PAP P O3 SING N N 26 PAP O2 HO2 SING N N 27 PAP O3 HO3 SING N N 28 PAP "C2'" "O2'" SING N N 29 PAP "C2'" "C1'" SING N N 30 PAP "C2'" "H2'" SING N N 31 PAP "O2'" "HO2'" SING N N 32 PAP "C1'" N9 SING N N 33 PAP "C1'" "H1'" SING N N 34 PAP N9 C8 SING Y N 35 PAP N9 C4 SING Y N 36 PAP C8 N7 DOUB Y N 37 PAP C8 H8 SING N N 38 PAP N7 C5 SING Y N 39 PAP C5 C6 SING Y N 40 PAP C5 C4 DOUB Y N 41 PAP C6 N6 SING N N 42 PAP C6 N1 DOUB Y N 43 PAP N6 HN61 SING N N 44 PAP N6 HN62 SING N N 45 PAP N1 C2 SING Y N 46 PAP C2 N3 DOUB Y N 47 PAP C2 H2 SING N N 48 PAP N3 C4 SING Y N 49 # 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 PAP SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O" PAP SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P](O)(O)=O)[C@@H](O[P](O)(O)=O)[C@H]3O" PAP SMILES CACTVS 3.341 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH]3O" PAP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)OP(=O)(O)O)OP(=O)(O)O)O)N" PAP SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)OP(=O)(O)O)O)N" PAP InChI InChI 1.03 "InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-6(16)7(27-29(17,18)19)4(26-10)1-25-31(23,24)28-30(20,21)22/h2-4,6-7,10,16H,1H2,(H,23,24)(H2,11,12,13)(H2,17,18,19)(H2,20,21,22)/t4-,6-,7-,10-/m1/s1" PAP InChIKey InChI 1.03 GBBWIZKLHXYJOA-KQYNXXCUSA-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 PAP "SYSTEMATIC NAME" ACDLabs 10.04 ;adenosine 3'-(dihydrogen phosphate) 5'-(trihydrogen diphosphate) ; PAP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxy-oxolan-2-yl]methyl 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 PAP "Create component" 1999-07-08 RCSB PAP "Modify descriptor" 2011-06-04 RCSB #