data_APR # _chem_comp.id APR _chem_comp.name ADENOSINE-5-DIPHOSPHORIBOSE _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H23 N5 O14 P2" _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 2024-09-27 _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 559.316 _chem_comp.one_letter_code ? _chem_comp.three_letter_code APR _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 1G9Q _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm Y # 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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 APR N1 N1 N 0 1 Y N N N N N 57.304 21.677 3.126 2.348 -0.932 9.041 N1 APR 1 APR C2 C2 C 0 1 Y N N N N N 58.333 20.780 2.780 1.265 -1.622 8.731 C2 APR 2 APR N3 N3 N 0 1 Y N N N N N 58.815 19.783 3.523 0.592 -1.418 7.618 N3 APR 3 APR C4 C4 C 0 1 Y N N N N N 58.161 19.655 4.774 0.984 -0.493 6.749 C4 APR 4 APR C5 C5 C 0 1 Y N N N N N 57.100 20.441 5.267 2.128 0.271 7.035 C5 APR 5 APR C6 C6 C 0 1 Y N N N N N 56.684 21.562 4.396 2.816 0.012 8.233 C6 APR 6 APR N6 N6 N 0 1 N N N N N N 55.837 22.531 4.767 3.952 0.730 8.566 N6 APR 7 APR N7 N7 N 0 1 Y N N N N N 56.714 19.987 6.521 2.307 1.124 5.999 N7 APR 8 APR C8 C8 C 0 1 Y N N N N N 57.592 19.016 6.814 1.365 0.943 5.120 C8 APR 9 APR N9 N9 N 0 1 Y N N N N N 58.523 18.831 5.825 0.523 -0.044 5.537 N9 APR 10 APR "C1'" C1* C 0 1 N N R N N N 59.925 18.013 5.799 -0.656 -0.537 4.822 "C1'" APR 11 APR "C2'" C2* C 0 1 N N R N N N 60.873 18.577 6.883 -1.902 0.290 5.207 "C2'" APR 12 APR "O2'" O2* O 0 1 N N N N N N 62.159 18.740 6.323 -2.672 -0.385 6.202 "O2'" APR 13 APR "C3'" C3* C 0 1 N N S N N N 60.931 17.488 8.019 -2.700 0.400 3.886 "C3'" APR 14 APR "O3'" O3* O 0 1 N N N N N N 62.274 17.237 8.416 -3.986 -0.206 4.025 "O3'" APR 15 APR "O4'" O4* O 0 1 N N N N N N 59.714 16.695 6.161 -0.502 -0.338 3.400 "O4'" APR 16 APR "C4'" C4* C 0 1 N N R N N N 60.320 16.270 7.470 -1.842 -0.377 2.863 "C4'" APR 17 APR "C5'" C5* C 0 1 N N N N N N 59.249 15.847 8.393 -1.888 0.307 1.496 "C5'" APR 18 APR "O5'" O5* O 0 1 N N N N N N 58.071 15.548 7.636 -1.032 -0.386 0.586 "O5'" APR 19 APR PA PA P 0 1 N N S N N N 56.778 15.038 8.330 -1.129 0.384 -0.823 PA APR 20 APR O1A O1A O 0 1 N N N N N N 56.709 13.669 8.178 -0.686 1.786 -0.651 O1A APR 21 APR O2A O2A O 0 1 N N N N N N 55.711 15.657 7.705 -2.652 0.362 -1.343 O2A APR 22 APR O3A O3A O 0 1 N N N N N N 56.727 15.443 9.983 -0.183 -0.348 -1.901 O3A APR 23 APR PB PB P 0 1 N N R N N N 56.585 16.854 10.752 -0.328 0.470 -3.280 PB APR 24 APR O1B O1B O 0 1 N N N N N N 57.185 17.940 9.929 0.101 1.871 -3.069 O1B APR 25 APR O2B O2B O 0 1 N N N N N N 57.257 16.795 12.071 -1.865 0.447 -3.758 O2B APR 26 APR O5D RO5* O 0 1 N N N N N N 54.938 17.195 10.904 0.595 -0.210 -4.408 O5D APR 27 APR C5D RC5* C 0 1 N N N N N N 54.343 16.628 12.167 0.423 0.556 -5.601 C5D APR 28 APR O4D RO4* O 0 1 N N N N N N 54.107 19.129 12.819 0.853 -1.385 -6.996 O4D APR 29 APR O1D RO1* O 0 1 N N N N N N 52.862 20.438 11.386 0.208 -2.680 -8.863 O1D APR 30 APR C1D RC1* C 0 1 N N R N N N 52.834 19.759 12.610 1.030 -1.602 -8.412 C1D APR 31 APR O2D RO2* O 0 1 N N N N N N 50.542 19.075 13.137 1.185 -0.064 -10.319 O2D APR 32 APR C2D RC2* C 0 1 N N R N N N 51.779 18.629 12.553 0.574 -0.261 -9.042 C2D APR 33 APR O3D RO3* O 0 1 N N N N N N 51.951 17.595 14.816 2.341 1.326 -8.446 O3D APR 34 APR C3D RC3* C 0 1 N N S N N N 52.364 17.465 13.367 1.096 0.775 -8.014 C3D APR 35 APR C4D RC4* C 0 1 N N R N N N 53.842 17.623 13.261 1.279 -0.041 -6.720 C4D APR 36 APR H2 H2 H 0 1 N N N N N N 58.826 20.870 1.797 0.918 -2.381 9.417 H2 APR 37 APR H61 1H6 H 0 1 N N N N N N 55.391 22.448 5.680 4.416 0.544 9.397 H61 APR 38 APR H62 2H6 H 0 1 N N N N N N 55.118 22.640 4.051 4.286 1.415 7.966 H62 APR 39 APR H8 H8 H 0 1 N N N N N N 57.553 18.439 7.753 1.265 1.493 4.196 H8 APR 40 APR "H'1" 1H* H 0 1 N N N N N N 60.348 18.101 4.771 -0.819 -1.592 5.042 "H'1" APR 41 APR "H'2" 2H* H 0 1 N N N N N N 60.523 19.560 7.276 -1.608 1.279 5.559 "H'2" APR 42 APR "HO'2" 2HO* H 0 0 N N N N N N 62.741 19.086 6.988 -3.464 0.149 6.354 "HO'2" APR 43 APR "H'3" 3H* H 0 1 N N N N N N 60.384 17.837 8.926 -2.801 1.443 3.585 "H'3" APR 44 APR "HO'3" 3HO* H 0 0 N N N N N N 62.309 16.580 9.101 -4.474 0.319 4.673 "HO'3" APR 45 APR "H'4" 4H* H 0 1 N N N N N N 61.043 15.432 7.339 -2.189 -1.407 2.782 "H'4" APR 46 APR "H5'1" 1H5* H 0 0 N N N N N N 59.561 14.998 9.044 -2.910 0.293 1.116 "H5'1" APR 47 APR "H5'2" 2H5* H 0 0 N N N N N N 59.058 16.598 9.194 -1.552 1.340 1.595 "H5'2" APR 48 APR HOA2 2HOA H 0 0 N N N N N N 54.920 15.345 8.129 -2.901 -0.566 -1.442 HOA2 APR 49 APR HOB2 2HOB H 0 0 N N N N N N 57.173 17.625 12.523 -2.105 -0.480 -3.884 HOB2 APR 50 APR H5R1 1H5R H 0 0 N N N N N N 53.512 15.935 11.898 -0.625 0.539 -5.897 H5R1 APR 51 APR H5R2 2H5R H 0 0 N N N N N N 55.071 15.919 12.626 0.732 1.586 -5.418 H5R2 APR 52 APR HOR1 1HOR H 0 0 N N N N N N 52.019 20.854 11.247 0.495 -3.469 -8.385 HOR1 APR 53 APR "HR'1" 1HR* H 0 0 N N N N N N 52.595 20.484 13.422 2.078 -1.797 -8.642 "HR'1" APR 54 APR HOR2 2HOR H 0 0 N N N N N N 49.894 18.381 13.102 0.892 -0.792 -10.884 HOR2 APR 55 APR "HR'2" 2HR* H 0 0 N N N N N N 51.559 18.323 11.503 -0.512 -0.219 -9.122 "HR'2" APR 56 APR HOR3 3HOR H 0 0 N N N N N N 52.312 16.875 15.319 2.172 1.772 -9.288 HOR3 APR 57 APR "HR'3" 3HR* H 0 0 N N N N N N 52.011 16.474 12.994 0.361 1.567 -7.864 "HR'3" APR 58 APR "HR'4" 4HR* H 0 0 N N N N N N 54.373 17.409 14.217 2.329 -0.038 -6.425 "HR'4" APR 59 # 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 APR N1 C2 SING Y N 1 APR N1 C6 DOUB Y N 2 APR C2 N3 DOUB Y N 3 APR C2 H2 SING N N 4 APR N3 C4 SING Y N 5 APR C4 C5 DOUB Y N 6 APR C4 N9 SING Y N 7 APR C5 C6 SING Y N 8 APR C5 N7 SING Y N 9 APR C6 N6 SING N N 10 APR N6 H61 SING N N 11 APR N6 H62 SING N N 12 APR N7 C8 DOUB Y N 13 APR C8 N9 SING Y N 14 APR C8 H8 SING N N 15 APR N9 "C1'" SING N N 16 APR "C1'" "C2'" SING N N 17 APR "C1'" "O4'" SING N N 18 APR "C1'" "H'1" SING N N 19 APR "C2'" "O2'" SING N N 20 APR "C2'" "C3'" SING N N 21 APR "C2'" "H'2" SING N N 22 APR "O2'" "HO'2" SING N N 23 APR "C3'" "O3'" SING N N 24 APR "C3'" "C4'" SING N N 25 APR "C3'" "H'3" SING N N 26 APR "O3'" "HO'3" SING N N 27 APR "O4'" "C4'" SING N N 28 APR "C4'" "C5'" SING N N 29 APR "C4'" "H'4" SING N N 30 APR "C5'" "O5'" SING N N 31 APR "C5'" "H5'1" SING N N 32 APR "C5'" "H5'2" SING N N 33 APR "O5'" PA SING N N 34 APR PA O1A DOUB N N 35 APR PA O2A SING N N 36 APR PA O3A SING N N 37 APR O2A HOA2 SING N N 38 APR O3A PB SING N N 39 APR PB O1B DOUB N N 40 APR PB O2B SING N N 41 APR PB O5D SING N N 42 APR O2B HOB2 SING N N 43 APR O5D C5D SING N N 44 APR C5D C4D SING N N 45 APR C5D H5R1 SING N N 46 APR C5D H5R2 SING N N 47 APR O4D C1D SING N N 48 APR O4D C4D SING N N 49 APR O1D C1D SING N N 50 APR O1D HOR1 SING N N 51 APR C1D C2D SING N N 52 APR C1D "HR'1" SING N N 53 APR O2D C2D SING N N 54 APR O2D HOR2 SING N N 55 APR C2D C3D SING N N 56 APR C2D "HR'2" SING N N 57 APR O3D C3D SING N N 58 APR O3D HOR3 SING N N 59 APR C3D C4D SING N N 60 APR C3D "HR'3" SING N N 61 APR C4D "HR'4" SING N N 62 # 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 APR SMILES ACDLabs 10.04 "O=P(O)(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)OP(=O)(O)OCC4OC(O)C(O)C4O" APR SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O" APR SMILES CACTVS 3.341 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O" APR 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)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)O)O)O)O)O)N" APR SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N" APR InChI InChI 1.03 "InChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15-/m1/s1" APR InChIKey InChI 1.03 SRNWOUGRCWSEMX-KEOHHSTQSA-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 APR "SYSTEMATIC NAME" ACDLabs 10.04 "[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5R)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)" APR "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2R,3S,4R,5R)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] 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 APR "Create component" 1999-07-08 RCSB APR "Modify descriptor" 2011-06-04 RCSB APR "Modify PCM" 2024-09-27 PDBE # loop_ _pdbx_chem_comp_pcm.pcm_id _pdbx_chem_comp_pcm.comp_id _pdbx_chem_comp_pcm.modified_residue_id _pdbx_chem_comp_pcm.type _pdbx_chem_comp_pcm.category _pdbx_chem_comp_pcm.position _pdbx_chem_comp_pcm.polypeptide_position _pdbx_chem_comp_pcm.comp_id_linking_atom _pdbx_chem_comp_pcm.modified_residue_id_linking_atom _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession 1 APR ARG ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D NH1 ? PTM-0053 2 APR ASN ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D ND2 ? PTM-0054 3 APR ASP ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D OD2 ? PTM-0497 4 APR CYS ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D SG ? PTM-0055 5 APR DDE ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D NE2 ? PTM-0672 6 APR GLU ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D OE2 ? PTM-0646 7 APR GLY ADP-ribosylation ADP-ribose "Amino-acid backbone" C-terminal C1D OXT ? PTM-0671 8 APR HIS ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D NE2 ? PTM-0720 9 APR SER ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D OG ? PTM-0056 10 APR THR ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D OG1 ? PTM-0721 11 APR TYR ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D OH ? PTM-0670 12 APR LYS ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D NZ ? PTM-0355 #