data_XYQ # _chem_comp.id XYQ _chem_comp.name "(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL ACETATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H25 N5 O15 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ACETYL-RIBOSYL-ADP _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2006-07-13 _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 601.352 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XYQ _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 ? _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 XYQ O5 O5 O 0 1 N N N N N N -0.359 39.124 84.350 -7.889 1.042 -3.134 O5 XYQ 1 XYQ CH CH C 0 1 N N N N N N -0.456 39.139 85.683 -8.361 1.931 -2.464 CH XYQ 2 XYQ CH3 CH3 C 0 1 N N N N N N 0.730 39.155 86.487 -8.775 3.226 -3.115 CH3 XYQ 3 XYQ OH OH O 0 1 N N N N N N -1.698 39.087 86.328 -8.516 1.764 -1.142 OH XYQ 4 XYQ C1N C1N C 0 1 N N R N N N -1.665 38.933 87.761 -8.118 0.517 -0.515 C1N XYQ 5 XYQ C2N C2N C 0 1 N N R N N N -1.907 37.439 87.981 -8.619 0.480 0.945 C2N XYQ 6 XYQ C3N C3N C 0 1 N N S N N N -3.392 37.345 88.015 -7.425 -0.186 1.685 C3N XYQ 7 XYQ O3N O3N O 0 1 N N N N N N -3.869 36.983 86.685 -7.363 0.237 3.049 O3N XYQ 8 XYQ O2N O2N O 0 1 N N N N N N -1.223 36.535 87.161 -8.852 1.800 1.439 O2N XYQ 9 XYQ O4N O4N O 0 1 N N N N N N -2.827 39.638 88.009 -6.689 0.422 -0.486 O4N XYQ 10 XYQ C4N C4N C 0 1 N N R N N N -3.903 38.715 88.222 -6.228 0.370 0.873 C4N XYQ 11 XYQ C5N C5N C 0 1 N N N N N N -4.349 38.784 89.699 -5.024 -0.568 0.990 C5N XYQ 12 XYQ O5N O5N O 0 1 N N N N N N -5.606 38.139 89.849 -3.917 -0.012 0.277 O5N XYQ 13 XYQ PN PN P 0 1 N N R N N N -5.873 37.012 90.997 -2.693 -1.045 0.442 PN XYQ 14 XYQ ON2 ON2 O 0 1 N N N N N N -4.740 36.078 91.073 -3.059 -2.432 -0.289 ON2 XYQ 15 XYQ ON1 ON1 O 0 1 N N N N N N -7.255 36.600 90.834 -2.447 -1.294 1.880 ON1 XYQ 16 XYQ ON3 ON3 O 0 1 N N N N N N -5.681 37.923 92.320 -1.369 -0.419 -0.228 ON3 XYQ 17 XYQ PA PA P 0 1 N N R N N N -6.798 38.912 92.951 -0.122 -1.286 0.307 PA XYQ 18 XYQ OA2 OA2 O 0 1 N N N N N N -6.003 39.618 93.994 0.193 -0.887 1.834 OA2 XYQ 19 XYQ O5A O5A O 0 1 N N N N N N -7.927 37.989 93.523 1.170 -0.986 -0.605 O5A XYQ 20 XYQ C5A C5A C 0 1 N N N N N N -7.730 37.201 94.708 2.204 -1.866 -0.159 C5A XYQ 21 XYQ C4A C4A C 0 1 N N R N N N -9.048 36.584 95.072 3.468 -1.631 -0.988 C4A XYQ 22 XYQ O4A O4A O 0 1 N N N N N N -8.893 35.536 96.052 3.994 -0.321 -0.716 O4A XYQ 23 XYQ C1A C1A C 0 1 N N R N N N -9.618 35.894 97.258 5.432 -0.419 -0.801 C1A XYQ 24 XYQ N9 N9 N 0 1 Y N N N N N -8.875 35.334 98.387 6.068 0.680 -0.070 N9 XYQ 25 XYQ C8 C8 C 0 1 Y N N N N N -7.735 35.780 98.970 5.516 1.397 0.949 C8 XYQ 26 XYQ N7 N7 N 0 1 Y N N N N N -7.350 34.875 99.932 6.359 2.296 1.368 N7 XYQ 27 XYQ C5 C5 C 0 1 Y N N N N N -8.245 33.889 99.883 7.502 2.214 0.645 C5 XYQ 28 XYQ C4 C4 C 0 1 Y N N N N N -9.130 34.152 98.899 7.331 1.172 -0.283 C4 XYQ 29 XYQ N3 N3 N 0 1 Y N N N N N -10.227 33.291 98.602 8.319 0.890 -1.125 N3 XYQ 30 XYQ C2 C2 C 0 1 Y N N N N N -10.320 32.122 99.275 9.448 1.567 -1.088 C2 XYQ 31 XYQ N1 N1 N 0 1 Y N N N N N -9.374 31.868 100.211 9.656 2.550 -0.231 N1 XYQ 32 XYQ C6 C6 C 0 1 Y N N N N N -8.382 32.698 100.519 8.724 2.908 0.646 C6 XYQ 33 XYQ N6 N6 N 0 1 N N N N N N -7.391 32.465 101.428 8.952 3.939 1.541 N6 XYQ 34 XYQ C2A C2A C 0 1 N N R N N N -10.053 37.374 97.173 5.743 -1.780 -0.127 C2A XYQ 35 XYQ C3A C3A C 0 1 N N S N N N -9.898 37.678 95.682 4.551 -2.654 -0.595 C3A XYQ 36 XYQ O3A O3A O 0 1 N N N N N N -11.187 37.406 95.070 4.927 -3.451 -1.720 O3A XYQ 37 XYQ O2A O2A O 0 1 N N N N N N -11.319 37.542 97.718 6.982 -2.312 -0.600 O2A XYQ 38 XYQ OA1 OA1 O 0 1 N N N N N N -7.472 39.767 91.881 -0.455 -2.726 0.231 OA1 XYQ 39 XYQ HH31 1HH3 H 0 0 N N N N N N 0.751 38.261 87.127 -8.574 3.175 -4.185 HH31 XYQ 40 XYQ HH32 2HH3 H 0 0 N N N N N N 0.734 40.057 87.116 -9.840 3.390 -2.952 HH32 XYQ 41 XYQ HH33 3HH3 H 0 0 N N N N N N 1.616 39.159 85.835 -8.210 4.049 -2.678 HH33 XYQ 42 XYQ H1N H1N H 0 1 N N N N N N -0.783 39.244 88.340 -8.532 -0.325 -1.070 H1N XYQ 43 XYQ H2N H2N H 0 1 N N N N N N -1.444 37.086 88.914 -9.518 -0.130 1.033 H2N XYQ 44 XYQ H3N H3N H 0 1 N N N N N N -3.707 36.625 88.785 -7.477 -1.272 1.615 H3N XYQ 45 XYQ HO3N HO3N H 0 0 N N N N N N -4.816 36.904 86.698 -8.133 -0.142 3.494 HO3N XYQ 46 XYQ HO2N HO2N H 0 0 N N N N N N -1.068 36.932 86.312 -9.601 2.157 0.942 HO2N XYQ 47 XYQ H4N H4N H 0 1 N N N N N N -4.730 38.960 87.539 -5.964 1.368 1.222 H4N XYQ 48 XYQ H5N1 1H5N H 0 0 N N N N N N -4.440 39.837 90.004 -4.757 -0.688 2.040 H5N1 XYQ 49 XYQ H5N2 2H5N H 0 0 N N N N N N -3.602 38.281 90.330 -5.278 -1.540 0.566 H5N2 XYQ 50 XYQ HON2 HON2 H 0 0 N N N N N N -4.436 35.877 90.196 -3.211 -2.226 -1.221 HON2 XYQ 51 XYQ HOA2 HOA2 H 0 0 N N N N N N -5.122 39.768 93.673 0.404 0.056 1.839 HOA2 XYQ 52 XYQ H5A1 1H5A H 0 0 N N N N N N -7.361 37.831 95.531 2.418 -1.672 0.893 H5A1 XYQ 53 XYQ H5A2 2H5A H 0 0 N N N N N N -6.985 36.414 94.518 1.878 -2.899 -0.279 H5A2 XYQ 54 XYQ H4A H4A H 0 1 N N N N N N -9.503 36.146 94.171 3.237 -1.724 -2.049 H4A XYQ 55 XYQ H1A H1A H 0 1 N N N N N N -10.610 35.445 97.414 5.755 -0.424 -1.842 H1A XYQ 56 XYQ H8 H8 H 0 1 N N N N N N -7.216 36.694 98.721 4.526 1.241 1.351 H8 XYQ 57 XYQ H2 H2 H 0 1 N N N N N N -11.116 31.420 99.075 10.232 1.309 -1.784 H2 XYQ 58 XYQ HN61 1HN6 H 0 0 N N N N N N -7.365 33.213 102.092 8.263 4.190 2.176 HN61 XYQ 59 XYQ HN62 2HN6 H 0 0 N N N N N N -6.511 32.408 100.956 9.799 4.410 1.532 HN62 XYQ 60 XYQ H2A H2A H 0 1 N N N N N N -9.461 38.089 97.763 5.753 -1.682 0.959 H2A XYQ 61 XYQ H3A H3A H 0 1 N N N N N N -9.506 38.696 95.544 4.199 -3.288 0.219 H3A XYQ 62 XYQ HO3A HO3A H 0 0 N N N N N N -11.852 37.347 95.745 5.646 -4.027 -1.427 HO3A XYQ 63 XYQ HO2A HO2A H 0 0 N N N N N N -11.254 37.580 98.665 7.116 -3.154 -0.144 HO2A XYQ 64 # 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 XYQ O5 CH DOUB N N 1 XYQ CH CH3 SING N N 2 XYQ CH OH SING N N 3 XYQ CH3 HH31 SING N N 4 XYQ CH3 HH32 SING N N 5 XYQ CH3 HH33 SING N N 6 XYQ OH C1N SING N N 7 XYQ C1N C2N SING N N 8 XYQ C1N O4N SING N N 9 XYQ C1N H1N SING N N 10 XYQ C2N C3N SING N N 11 XYQ C2N O2N SING N N 12 XYQ C2N H2N SING N N 13 XYQ C3N O3N SING N N 14 XYQ C3N C4N SING N N 15 XYQ C3N H3N SING N N 16 XYQ O3N HO3N SING N N 17 XYQ O2N HO2N SING N N 18 XYQ O4N C4N SING N N 19 XYQ C4N C5N SING N N 20 XYQ C4N H4N SING N N 21 XYQ C5N O5N SING N N 22 XYQ C5N H5N1 SING N N 23 XYQ C5N H5N2 SING N N 24 XYQ O5N PN SING N N 25 XYQ PN ON2 SING N N 26 XYQ PN ON1 DOUB N N 27 XYQ PN ON3 SING N N 28 XYQ ON2 HON2 SING N N 29 XYQ ON3 PA SING N N 30 XYQ PA OA2 SING N N 31 XYQ PA O5A SING N N 32 XYQ PA OA1 DOUB N N 33 XYQ OA2 HOA2 SING N N 34 XYQ O5A C5A SING N N 35 XYQ C5A C4A SING N N 36 XYQ C5A H5A1 SING N N 37 XYQ C5A H5A2 SING N N 38 XYQ C4A O4A SING N N 39 XYQ C4A C3A SING N N 40 XYQ C4A H4A SING N N 41 XYQ O4A C1A SING N N 42 XYQ C1A N9 SING N N 43 XYQ C1A C2A SING N N 44 XYQ C1A H1A SING N N 45 XYQ N9 C8 SING Y N 46 XYQ N9 C4 SING Y N 47 XYQ C8 N7 DOUB Y N 48 XYQ C8 H8 SING N N 49 XYQ N7 C5 SING Y N 50 XYQ C5 C4 SING Y N 51 XYQ C5 C6 DOUB Y N 52 XYQ C4 N3 DOUB Y N 53 XYQ N3 C2 SING Y N 54 XYQ C2 N1 DOUB Y N 55 XYQ C2 H2 SING N N 56 XYQ N1 C6 SING Y N 57 XYQ C6 N6 SING N N 58 XYQ N6 HN61 SING N N 59 XYQ N6 HN62 SING N N 60 XYQ C2A C3A SING N N 61 XYQ C2A O2A SING N N 62 XYQ C2A H2A SING N N 63 XYQ C3A O3A SING N N 64 XYQ C3A H3A SING N N 65 XYQ O3A HO3A SING N N 66 XYQ O2A HO2A SING N N 67 # 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 XYQ SMILES ACDLabs 10.04 "O=C(OC1OC(C(O)C1O)COP(=O)(O)OP(=O)(O)OCC4OC(n2c3ncnc(N)c3nc2)C(O)C4O)C" XYQ SMILES_CANONICAL CACTVS 3.341 "CC(=O)O[C@H]1O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34)[C@@H](O)[C@H]1O" XYQ SMILES CACTVS 3.341 "CC(=O)O[CH]1O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34)[CH](O)[CH]1O" XYQ SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC(=O)O[C@@H]1[C@@H]([C@@H]([C@H](O1)CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)O)O" XYQ SMILES "OpenEye OEToolkits" 1.5.0 "CC(=O)OC1C(C(C(O1)COP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O)O)O" XYQ InChI InChI 1.03 "InChI=1S/C17H25N5O15P2/c1-6(23)34-17-13(27)11(25)8(36-17)3-33-39(30,31)37-38(28,29)32-2-7-10(24)12(26)16(35-7)22-5-21-9-14(18)19-4-20-15(9)22/h4-5,7-8,10-13,16-17,24-27H,2-3H2,1H3,(H,28,29)(H,30,31)(H2,18,19,20)/t7-,8-,10-,11-,12-,13-,16-,17+/m1/s1" XYQ InChIKey InChI 1.03 IJOUKWCBVUMMCR-DLFWLGJNSA-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 XYQ "SYSTEMATIC NAME" ACDLabs 10.04 "(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxytetrahydrofuran-2-yl acetate (non-preferred name)" XYQ "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4S,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxymethyl]-3,4-dihydroxy-oxolan-2-yl] ethanoate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site XYQ "Create component" 2006-07-13 RCSB XYQ "Modify descriptor" 2011-06-04 RCSB XYQ "Modify synonyms" 2021-03-01 PDBE XYQ "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id XYQ _pdbx_chem_comp_synonyms.name ACETYL-RIBOSYL-ADP _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id XYQ _pdbx_chem_comp_pcm.modified_residue_id LYS _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom CH _pdbx_chem_comp_pcm.modified_residue_id_linking_atom NZ _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #