data_AR6 # _chem_comp.id AR6 _chem_comp.name "[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE" _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 Adenosine-5-Diphosphoribose _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2009-08-10 _chem_comp.pdbx_modified_date 2025-01-29 _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 AR6 _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 2WPS _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI _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 AR6 N1 N1 N 0 1 Y N N N N N -27.227 -0.488 -34.579 -8.232 3.116 0.345 N1 AR6 1 AR6 C2 C2 C 0 1 Y N N N N N -26.982 -1.058 -33.385 -8.022 2.281 1.347 C2 AR6 2 AR6 N3 N3 N 0 1 Y N N N N N -27.418 -0.522 -32.234 -7.005 1.445 1.368 N3 AR6 3 AR6 C4 C4 C 0 1 Y N N N N N -28.139 0.624 -32.218 -6.135 1.410 0.364 C4 AR6 4 AR6 C5 C5 C 0 1 Y N N N N N -28.451 1.306 -33.473 -6.315 2.279 -0.725 C5 AR6 5 AR6 C6 C6 C 0 1 Y N N N N N -27.935 0.661 -34.701 -7.415 3.153 -0.702 C6 AR6 6 AR6 N6 N6 N 0 1 N N N N N N -28.167 1.191 -35.920 -7.643 4.031 -1.747 N6 AR6 7 AR6 N7 N7 N 0 1 Y N N N N N -29.180 2.399 -33.151 -5.304 2.042 -1.596 N7 AR6 8 AR6 C8 C8 C 0 1 Y N N N N N -29.308 2.419 -31.802 -4.535 1.105 -1.122 C8 AR6 9 AR6 N9 N9 N 0 1 Y N N N N N -28.677 1.361 -31.260 -5.006 0.683 0.086 N9 AR6 10 AR6 PA PA P 0 1 N N N N N N -30.937 5.146 -26.734 0.814 -2.273 -0.782 PA AR6 11 AR6 PB PB P 0 1 N N N N N N -33.759 5.142 -26.881 3.292 -0.786 -1.442 PB AR6 12 AR6 "C1'" "C1'" C 0 1 N N R N N N -28.595 1.000 -29.827 -4.414 -0.357 0.931 "C1'" AR6 13 AR6 O1A O1A O 0 1 N N N N N N -30.966 5.333 -25.232 1.339 -3.723 -0.319 O1A AR6 14 AR6 O1B O1B O 0 1 N N N N N N -34.561 4.556 -28.010 2.859 0.174 -2.659 O1B AR6 15 AR6 C1D C1D C 0 1 N N S N N N -34.026 3.465 -21.791 7.806 0.743 1.993 C1D AR6 16 AR6 O1D O1D O 0 1 N Y N N N N -33.895 2.242 -21.057 7.282 1.453 3.117 O1D AR6 17 AR6 "C2'" "C2'" C 0 1 N N R N N N -27.710 1.946 -29.048 -5.091 -1.726 0.668 "C2'" AR6 18 AR6 "O2'" "O2'" O 0 1 N N N N N N -26.333 1.550 -29.145 -6.262 -1.878 1.472 "O2'" AR6 19 AR6 O2A O2A O 0 1 N N N N N N -30.644 6.243 -27.719 0.420 -2.322 -2.208 O2A AR6 20 AR6 O2B O2B O 0 1 N N N N N N -33.741 6.610 -26.586 3.926 -2.010 -1.980 O2B AR6 21 AR6 C2D C2D C 0 1 N N R N N N -35.433 3.591 -22.339 8.538 1.718 1.051 C2D AR6 22 AR6 O2D O2D O 0 1 N N N N N N -36.402 2.982 -21.482 8.509 3.044 1.583 O2D AR6 23 AR6 "C3'" "C3'" C 0 1 N N S N N N -28.298 1.842 -27.654 -3.989 -2.722 1.104 "C3'" AR6 24 AR6 "O3'" "O3'" O 0 1 N N N N N N -27.778 0.716 -26.948 -4.227 -3.180 2.437 "O3'" AR6 25 AR6 O3A O3A O 0 1 N N N N N N -32.329 4.565 -27.218 1.988 -1.189 -0.587 O3A AR6 26 AR6 C3D C3D C 0 1 N N S N N N -35.377 2.898 -23.687 7.732 1.646 -0.269 C3D AR6 27 AR6 O3D O3D O 0 1 N N N N N N -36.029 1.640 -23.707 7.582 2.945 -0.846 O3D AR6 28 AR6 "C4'" "C4'" C 0 1 N N R N N N -29.779 1.615 -27.916 -2.688 -1.898 1.041 "C4'" AR6 29 AR6 "O4'" "O4'" O 0 1 N N N N N N -29.889 1.066 -29.228 -3.036 -0.587 0.565 "O4'" AR6 30 AR6 C4D C4D C 0 1 N N R N N N -33.900 2.647 -23.920 6.367 1.093 0.213 C4D AR6 31 AR6 O4D O4D O 0 1 N N N N N N -33.181 3.390 -22.935 6.731 0.151 1.245 O4D AR6 32 AR6 "C5'" "C5'" C 0 1 N N N N N N -30.606 2.885 -27.930 -1.701 -2.557 0.076 "C5'" AR6 33 AR6 "O5'" "O5'" O 0 1 N N N N N N -30.037 3.896 -27.105 -0.458 -1.853 0.112 "O5'" AR6 34 AR6 C5D C5D C 0 1 N N N N N N -33.511 3.083 -25.306 5.638 0.385 -0.931 C5D AR6 35 AR6 O5D O5D O 0 1 N N N N N N -34.124 4.345 -25.551 4.337 -0.012 -0.493 O5D AR6 36 AR6 H2 H2 H 0 1 N N N N N N -26.416 -1.977 -33.352 -8.710 2.284 2.179 H2 AR6 37 AR6 HN6 HN6 H 0 1 N N N N N N -27.749 0.613 -36.621 -8.407 4.629 -1.720 HN6 AR6 38 AR6 HN6A HN6A H 0 0 N N N N N N -29.153 1.245 -36.078 -7.040 4.048 -2.507 HN6A AR6 39 AR6 H8 H8 H 0 1 N N N N N N -29.840 3.175 -31.243 -3.654 0.720 -1.613 H8 AR6 40 AR6 "H1'" "H1'" H 0 1 N N N N N N -28.191 -0.019 -29.734 -4.493 -0.085 1.984 "H1'" AR6 41 AR6 H1D H1D H 0 1 N N N N N N -33.783 4.337 -21.166 8.494 -0.032 2.333 H1D AR6 42 AR6 "H2'" "H2'" H 0 1 N N N N N N -27.845 2.970 -29.426 -5.329 -1.846 -0.389 "H2'" AR6 43 AR6 "HO2'" "HO2'" H 0 0 N N N N N N -25.793 2.155 -28.650 -6.722 -2.719 1.343 "HO2'" AR6 44 AR6 H2D H2D H 0 1 N N N N N N -35.669 4.655 -22.489 9.566 1.394 0.891 H2D AR6 45 AR6 HO2D HO2D H 0 0 N N N N N N -37.268 3.083 -21.860 8.949 3.133 2.440 HO2D AR6 46 AR6 "H3'" "H3'" H 0 1 N N N N N N -28.145 2.780 -27.100 -3.943 -3.565 0.414 "H3'" AR6 47 AR6 "HO3'" "HO3'" H 0 0 N N N N N N -28.165 0.679 -26.081 -5.062 -3.655 2.546 "HO3'" AR6 48 AR6 H3D H3D H 0 1 N N N N N N -35.771 3.566 -24.468 8.203 0.962 -0.975 H3D AR6 49 AR6 HO3D HO3D H 0 0 N N N N N N -35.958 1.260 -24.575 8.418 3.370 -1.081 HO3D AR6 50 AR6 "H4'" "H4'" H 0 1 N N N N N N -30.183 0.920 -27.165 -2.247 -1.826 2.035 "H4'" AR6 51 AR6 H4D H4D H 0 1 N N N N N N -33.697 1.572 -23.809 5.752 1.894 0.624 H4D AR6 52 AR6 "H5'" "H5'" H 0 1 N N N N N N -30.665 3.260 -28.962 -1.540 -3.593 0.372 "H5'" AR6 53 AR6 "H5'A" "H5'A" H 0 0 N N N N N N -31.618 2.655 -27.565 -2.107 -2.527 -0.936 "H5'A" AR6 54 AR6 H5D H5D H 0 1 N N N N N N -32.417 3.178 -25.376 5.545 1.064 -1.778 H5D AR6 55 AR6 H5DA H5DA H 0 0 N N N N N N -33.863 2.346 -26.043 6.205 -0.496 -1.232 H5DA AR6 56 AR6 H1A H1A H 0 1 N N N N N N -30.772 6.239 -25.021 1.615 -3.764 0.607 H1A AR6 57 AR6 H1B H1B H 0 1 N N N N N N -35.021 5.251 -28.466 2.435 0.998 -2.379 H1B AR6 58 AR6 HD1 HD1 H 0 1 N N N N N N -33.011 2.170 -20.717 6.809 0.896 3.749 HD1 AR6 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 AR6 N1 C2 DOUB Y N 1 AR6 N1 C6 SING Y N 2 AR6 C2 N3 SING Y N 3 AR6 N3 C4 DOUB Y N 4 AR6 C4 C5 SING Y N 5 AR6 C4 N9 SING Y N 6 AR6 C5 C6 DOUB Y N 7 AR6 C5 N7 SING Y N 8 AR6 C6 N6 SING N N 9 AR6 N7 C8 DOUB Y N 10 AR6 C8 N9 SING Y N 11 AR6 N9 "C1'" SING N N 12 AR6 PA O1A SING N N 13 AR6 PA O2A DOUB N N 14 AR6 PA O3A SING N N 15 AR6 PA "O5'" SING N N 16 AR6 PB O1B SING N N 17 AR6 PB O2B DOUB N N 18 AR6 PB O3A SING N N 19 AR6 PB O5D SING N N 20 AR6 "C1'" "C2'" SING N N 21 AR6 "C1'" "O4'" SING N N 22 AR6 C1D O1D SING N N 23 AR6 C1D C2D SING N N 24 AR6 C1D O4D SING N N 25 AR6 "C2'" "O2'" SING N N 26 AR6 "C2'" "C3'" SING N N 27 AR6 C2D O2D SING N N 28 AR6 C2D C3D SING N N 29 AR6 "C3'" "O3'" SING N N 30 AR6 "C3'" "C4'" SING N N 31 AR6 C3D O3D SING N N 32 AR6 C3D C4D SING N N 33 AR6 "C4'" "O4'" SING N N 34 AR6 "C4'" "C5'" SING N N 35 AR6 C4D O4D SING N N 36 AR6 C4D C5D SING N N 37 AR6 "C5'" "O5'" SING N N 38 AR6 C5D O5D SING N N 39 AR6 C2 H2 SING N N 40 AR6 N6 HN6 SING N N 41 AR6 N6 HN6A SING N N 42 AR6 C8 H8 SING N N 43 AR6 "C1'" "H1'" SING N N 44 AR6 C1D H1D SING N N 45 AR6 "C2'" "H2'" SING N N 46 AR6 "O2'" "HO2'" SING N N 47 AR6 C2D H2D SING N N 48 AR6 O2D HO2D SING N N 49 AR6 "C3'" "H3'" SING N N 50 AR6 "O3'" "HO3'" SING N N 51 AR6 C3D H3D SING N N 52 AR6 O3D HO3D SING N N 53 AR6 "C4'" "H4'" SING N N 54 AR6 C4D H4D SING N N 55 AR6 "C5'" "H5'" SING N N 56 AR6 "C5'" "H5'A" SING N N 57 AR6 C5D H5D SING N N 58 AR6 C5D H5DA SING N N 59 AR6 O1A H1A SING N N 60 AR6 O1B H1B SING N N 61 AR6 O1D HD1 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 AR6 SMILES ACDLabs 12.01 "O=P(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)(O)OP(=O)(O)OCC4OC(O)C(O)C4O" AR6 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" AR6 InChIKey InChI 1.03 SRNWOUGRCWSEMX-ZQSHOCFMSA-N AR6 SMILES_CANONICAL CACTVS 3.370 "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" AR6 SMILES CACTVS 3.370 "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" AR6 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@H](O4)O)O)O)O)O)N" AR6 SMILES "OpenEye OEToolkits" 1.7.6 "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" # 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 AR6 "SYSTEMATIC NAME" ACDLabs 12.01 "[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5S)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)" AR6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5S)-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl 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 AR6 "Create component" 2009-08-10 EBI AR6 "Modify aromatic_flag" 2011-06-04 RCSB AR6 "Modify descriptor" 2011-06-04 RCSB AR6 "Modify leaving atom flag" 2013-06-20 RCSB AR6 "Other modification" 2019-09-05 EBI AR6 "Modify synonyms" 2020-06-05 PDBE AR6 "Modify PCM" 2024-09-27 PDBE AR6 "Modify PCM" 2025-01-29 PDBJ # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id AR6 _pdbx_chem_comp_synonyms.name Adenosine-5-Diphosphoribose _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # 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 AR6 ARG ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D NH1 PTM-0709 PTM-0053 2 AR6 ASN ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D ND2 ? PTM-0054 3 AR6 ASP ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D OD2 ? PTM-0497 4 AR6 CYS ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D SG ? PTM-0055 5 AR6 DDE ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D NE2 ? PTM-0672 6 AR6 GLU ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D OE2 ? PTM-0646 7 AR6 GLY ADP-ribosylation ADP-ribose "Amino-acid backbone" C-terminal C1D OXT ? PTM-0671 8 AR6 HIS ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D NE2 ? PTM-0720 9 AR6 SER ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D OG ? PTM-0056 10 AR6 THR ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D OG1 ? PTM-0721 11 AR6 TYR ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D OH ? PTM-0670 12 AR6 LYS ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D NZ ? PTM-0355 13 AR6 GLU ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D OE1 ? ? 14 AR6 ARG ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" O1D NH1 ? ? #