data_XYA # _chem_comp.id XYA _chem_comp.name "2-(6-AMINO-OCTAHYDRO-PURIN-9-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H13 N5 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms 9-BETA-D-XYLOFURANOSYL-ADENINE _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2003-06-23 _chem_comp.pdbx_modified_date 2021-03-01 _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 267.241 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XYA _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 1PR6 _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 XYA "O5'" "O5'" O 0 1 N N N 94.357 65.880 17.586 -4.519 1.826 -1.189 "O5'" XYA 1 XYA "C5'" "C5'" C 0 1 N N N 94.019 65.045 18.688 -4.276 0.880 -0.146 "C5'" XYA 2 XYA "C4'" "C4'" C 0 1 N N R 94.431 65.705 20.014 -3.129 -0.047 -0.556 "C4'" XYA 3 XYA "O4'" "O4'" O 0 1 N N N 93.719 66.925 20.239 -1.892 0.693 -0.643 "O4'" XYA 4 XYA "C1'" "C1'" C 0 1 N N R 92.551 66.686 21.079 -0.848 -0.299 -0.539 "C1'" XYA 5 XYA N9 N9 N 0 1 Y N N 91.438 67.218 20.222 0.411 0.327 -0.126 N9 XYA 6 XYA C8 C8 C 0 1 Y N N 91.299 68.535 19.904 0.545 1.517 0.525 C8 XYA 7 XYA N7 N7 N 0 1 Y N N 90.361 68.841 19.070 1.804 1.769 0.736 N7 XYA 8 XYA C5 C5 C 0 1 Y N N 89.790 67.602 18.786 2.556 0.757 0.240 C5 XYA 9 XYA C6 C6 C 0 1 Y N N 88.724 67.221 17.944 3.934 0.492 0.172 C6 XYA 10 XYA N1 N1 N 0 1 Y N N 88.377 65.898 17.866 4.334 -0.632 -0.413 N1 XYA 11 XYA C2 C2 C 0 1 Y N N 89.058 65.000 18.589 3.465 -1.484 -0.924 C2 XYA 12 XYA N3 N3 N 0 1 Y N N 90.097 65.249 19.425 2.166 -1.275 -0.888 N3 XYA 13 XYA C4 C4 C 0 1 Y N N 90.423 66.585 19.483 1.672 -0.178 -0.324 C4 XYA 14 XYA N6 N6 N 0 1 N N N 88.061 68.121 17.232 4.853 1.379 0.705 N6 XYA 15 XYA "C2'" "C2'" C 0 1 N N R 92.617 65.175 21.405 -1.340 -1.282 0.546 "C2'" XYA 16 XYA "O2'" "O2'" O 0 1 N N N 92.250 64.890 22.747 -0.985 -2.626 0.212 "O2'" XYA 17 XYA "C3'" "C3'" C 0 1 N N R 94.100 64.899 21.231 -2.878 -1.110 0.535 "C3'" XYA 18 XYA "O3'" "O3'" O 0 1 N N N 94.463 63.557 21.055 -3.342 -0.645 1.804 "O3'" XYA 19 XYA "H5'" "H5'" H 0 1 N N N 94.102 65.472 16.767 -5.247 2.389 -0.891 "H5'" XYA 20 XYA "H5'1" "1H5'" H 0 0 N N N 94.453 64.024 18.582 -5.176 0.290 0.026 "H5'1" XYA 21 XYA "H5'2" "2H5'" H 0 0 N N N 92.939 64.769 18.682 -4.007 1.408 0.768 "H5'2" XYA 22 XYA "H4'" "H4'" H 0 1 N N N 95.532 65.833 19.894 -3.352 -0.526 -1.509 "H4'" XYA 23 XYA "H1'" "H1'" H 0 1 N N N 92.442 67.174 22.075 -0.719 -0.816 -1.490 "H1'" XYA 24 XYA H8 H8 H 0 1 N N N 91.934 69.338 20.314 -0.274 2.156 0.821 H8 XYA 25 XYA H2 H2 H 0 1 N N N 88.731 63.952 18.486 3.833 -2.386 -1.390 H2 XYA 26 XYA HN61 1HN6 H 0 0 N N N 88.736 68.642 16.672 5.802 1.183 0.655 HN61 XYA 27 XYA HN62 2HN6 H 0 0 N N N 87.290 67.846 16.623 4.549 2.199 1.125 HN62 XYA 28 XYA "H2'" "H2'" H 0 1 N N N 91.928 64.569 20.773 -0.932 -1.011 1.519 "H2'" XYA 29 XYA H1 H1 H 0 1 N N N 92.291 63.962 22.947 -1.372 -3.194 0.892 H1 XYA 30 XYA "H3'" "H3'" H 0 1 N N N 94.659 65.166 22.158 -3.364 -2.050 0.273 "H3'" XYA 31 XYA H3 H3 H 0 1 N N N 94.253 63.045 21.827 -4.294 -0.500 1.717 H3 XYA 32 # # 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 XYA "O5'" "C5'" SING N N 1 XYA "O5'" "H5'" SING N N 2 XYA "C5'" "C4'" SING N N 3 XYA "C5'" "H5'1" SING N N 4 XYA "C5'" "H5'2" SING N N 5 XYA "C4'" "O4'" SING N N 6 XYA "C4'" "C3'" SING N N 7 XYA "C4'" "H4'" SING N N 8 XYA "O4'" "C1'" SING N N 9 XYA "C1'" N9 SING N N 10 XYA "C1'" "C2'" SING N N 11 XYA "C1'" "H1'" SING N N 12 XYA N9 C8 SING Y N 13 XYA N9 C4 SING Y N 14 XYA C8 N7 DOUB Y N 15 XYA C8 H8 SING N N 16 XYA N7 C5 SING Y N 17 XYA C5 C6 DOUB Y N 18 XYA C5 C4 SING Y N 19 XYA C6 N1 SING Y N 20 XYA C6 N6 SING N N 21 XYA N1 C2 DOUB Y N 22 XYA C2 N3 SING Y N 23 XYA C2 H2 SING N N 24 XYA N3 C4 DOUB Y N 25 XYA N6 HN61 SING N N 26 XYA N6 HN62 SING N N 27 XYA "C2'" "O2'" SING N N 28 XYA "C2'" "C3'" SING N N 29 XYA "C2'" "H2'" SING N N 30 XYA "O2'" H1 SING N N 31 XYA "C3'" "O3'" SING N N 32 XYA "C3'" "H3'" SING N N 33 XYA "O3'" H3 SING N N 34 # # 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 XYA SMILES ACDLabs 10.04 "n2c1c(ncnc1n(c2)C3OC(C(O)C3O)CO)N" XYA SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@H](O)[C@H]3O" XYA SMILES CACTVS 3.341 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO)[CH](O)[CH]3O" XYA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]([C@H](O3)CO)O)O)N" XYA SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CO)O)O)N" XYA InChI InChI 1.03 "InChI=1S/C10H13N5O4/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(18)6(17)4(1-16)19-10/h2-4,6-7,10,16-18H,1H2,(H2,11,12,13)/t4-,6+,7-,10-/m1/s1" XYA InChIKey InChI 1.03 OIRDTQYFTABQOQ-GAWUUDPSSA-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 XYA "SYSTEMATIC NAME" ACDLabs 10.04 9-beta-D-xylofuranosyl-9H-purin-6-amine XYA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R,3R,4R,5R)-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site XYA "Create component" 2003-06-23 RCSB XYA "Modify descriptor" 2011-06-04 RCSB XYA "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id XYA _pdbx_chem_comp_synonyms.name 9-BETA-D-XYLOFURANOSYL-ADENINE _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##