data_XAD # _chem_comp.id XAD _chem_comp.name "9-(2,3-DIDEOXY-6-O-PHOSPHONO-BETA-D-ERYTHRO-HEXOPYRANOSYL)-9H-PURIN-6-AMINE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H16 N5 O6 P" _chem_comp.mon_nstd_parent_comp_id DA _chem_comp.pdbx_synonyms "2',3'-DI-DEOXY-BETA-D-GLUCOPYRANOSYL ADENINE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2006-06-20 _chem_comp.pdbx_modified_date 2020-06-17 _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 345.248 _chem_comp.one_letter_code A _chem_comp.three_letter_code XAD _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 2H9S _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 XAD OP3 O3P O 0 1 N Y N -16.283 9.480 12.323 -4.403 1.735 1.310 OP3 XAD 1 XAD P P P 0 1 N N N -17.059 10.187 13.539 -4.330 1.368 -0.256 P XAD 2 XAD OP1 O1P O 0 1 N N N -18.186 10.965 12.986 -5.410 0.413 -0.590 OP1 XAD 3 XAD OP2 O2P O 0 1 N N N -17.274 9.118 14.523 -4.511 2.709 -1.130 OP2 XAD 4 XAD "O6'" "O6'" O 0 1 N N N -16.055 11.231 14.161 -2.903 0.701 -0.586 "O6'" XAD 5 XAD "C6'" "C6'" C 0 1 N N N -14.801 10.769 14.637 -2.851 -0.537 0.125 "C6'" XAD 6 XAD "C5'" "C5'" C 0 1 N N R -13.724 11.759 14.272 -1.512 -1.226 -0.146 "C5'" XAD 7 XAD "C4'" "C4'" C 0 1 N N S -12.331 11.233 14.617 -1.508 -2.607 0.513 "C4'" XAD 8 XAD "O4'" "O4'" O 0 1 N N N -12.033 10.208 13.667 -2.585 -3.390 -0.005 "O4'" XAD 9 XAD "C3'" "C3'" C 0 1 N N N -11.325 12.390 14.530 -0.175 -3.301 0.209 "C3'" XAD 10 XAD "C2'" "C2'" C 0 1 N N N -11.768 13.596 15.342 0.969 -2.373 0.630 "C2'" XAD 11 XAD "C1'" "C1'" C 0 1 N N R -13.060 13.989 14.665 0.777 -1.009 -0.038 "C1'" XAD 12 XAD "O5'" "O5'" O 0 1 N N N -13.993 12.986 14.979 -0.455 -0.432 0.390 "O5'" XAD 13 XAD N9 N9 N 0 1 Y N N -13.705 15.202 15.119 1.884 -0.125 0.333 N9 XAD 14 XAD C8 C8 C 0 1 Y N N -14.103 15.479 16.409 1.887 0.781 1.352 C8 XAD 15 XAD N7 N7 N 0 1 Y N N -14.764 16.613 16.468 3.032 1.396 1.397 N7 XAD 16 XAD C5 C5 C 0 1 Y N N -14.883 17.029 15.141 3.838 0.922 0.417 C5 XAD 17 XAD C4 C4 C 0 1 Y N N -14.237 16.172 14.308 3.109 -0.055 -0.282 C4 XAD 18 XAD C6 C6 C 0 1 Y N N -15.473 18.141 14.538 5.146 1.207 -0.012 C6 XAD 19 XAD N6 N6 N 0 1 N N N -16.119 19.080 15.222 5.910 2.163 0.633 N6 XAD 20 XAD N1 N1 N 0 1 Y N N -15.408 18.260 13.183 5.633 0.532 -1.048 N1 XAD 21 XAD C2 C2 C 0 1 Y N N -14.766 17.327 12.451 4.911 -0.382 -1.670 C2 XAD 22 XAD N3 N3 N 0 1 Y N N -14.152 16.248 12.952 3.681 -0.678 -1.307 N3 XAD 23 XAD HOP3 3HOP H 0 0 N N N -16.885 9.340 11.601 -3.685 2.358 1.484 HOP3 XAD 24 XAD HOP2 2HOP H 0 0 N N N -17.320 8.281 14.077 -5.377 3.075 -0.903 HOP2 XAD 25 XAD "H6'1" "1H6'" H 0 0 N N N -14.573 9.796 14.178 -3.665 -1.181 -0.208 "H6'1" XAD 26 XAD "H6'2" "2H6'" H 0 0 N N N -14.843 10.661 15.731 -2.952 -0.347 1.194 "H6'2" XAD 27 XAD "H5'" "H5'" H 0 1 N N N -13.736 11.929 13.185 -1.374 -1.337 -1.222 "H5'" XAD 28 XAD "H4'" "H4'" H 0 1 N N N -12.280 10.824 15.637 -1.623 -2.496 1.591 "H4'" XAD 29 XAD "H4T'" "H4T'" H 0 0 N N N -11.967 10.589 12.799 -2.539 -4.251 0.432 "H4T'" XAD 30 XAD "H3'1" "1H3'" H 0 0 N N N -11.251 12.698 13.477 -0.106 -3.506 -0.860 "H3'1" XAD 31 XAD "H3'2" "2H3'" H 0 0 N N N -10.356 12.042 14.918 -0.113 -4.235 0.768 "H3'2" XAD 32 XAD "H2'1" "1H2'" H 0 0 N N N -11.023 14.405 15.362 1.921 -2.802 0.317 "H2'1" XAD 33 XAD "H2'2" "2H2'" H 0 0 N N N -11.921 13.343 16.401 0.961 -2.252 1.713 "H2'2" XAD 34 XAD "H1'" "H1'" H 0 1 N N N -12.787 14.134 13.609 0.761 -1.136 -1.121 "H1'" XAD 35 XAD H8 H8 H 0 1 N N N -13.898 14.847 17.260 1.059 0.961 2.022 H8 XAD 36 XAD HN61 1HN6 H 0 0 N N N -16.562 19.884 14.826 6.812 2.348 0.331 HN61 XAD 37 XAD HN62 2HN6 H 0 0 N N N -16.090 18.853 16.196 5.541 2.652 1.386 HN62 XAD 38 XAD H2 H2 H 0 1 N N N -14.746 17.460 11.379 5.347 -0.907 -2.508 H2 XAD 39 # # 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 XAD OP3 P SING N N 1 XAD OP3 HOP3 SING N N 2 XAD P OP1 DOUB N N 3 XAD P OP2 SING N N 4 XAD P "O6'" SING N N 5 XAD OP2 HOP2 SING N N 6 XAD "O6'" "C6'" SING N N 7 XAD "C6'" "C5'" SING N N 8 XAD "C6'" "H6'1" SING N N 9 XAD "C6'" "H6'2" SING N N 10 XAD "C5'" "C4'" SING N N 11 XAD "C5'" "O5'" SING N N 12 XAD "C5'" "H5'" SING N N 13 XAD "C4'" "O4'" SING N N 14 XAD "C4'" "C3'" SING N N 15 XAD "C4'" "H4'" SING N N 16 XAD "O4'" "H4T'" SING N N 17 XAD "C3'" "C2'" SING N N 18 XAD "C3'" "H3'1" SING N N 19 XAD "C3'" "H3'2" SING N N 20 XAD "C2'" "C1'" SING N N 21 XAD "C2'" "H2'1" SING N N 22 XAD "C2'" "H2'2" SING N N 23 XAD "C1'" "O5'" SING N N 24 XAD "C1'" N9 SING N N 25 XAD "C1'" "H1'" SING N N 26 XAD N9 C8 SING Y N 27 XAD N9 C4 SING Y N 28 XAD C8 N7 DOUB Y N 29 XAD C8 H8 SING N N 30 XAD N7 C5 SING Y N 31 XAD C5 C4 DOUB Y N 32 XAD C5 C6 SING Y N 33 XAD C4 N3 SING Y N 34 XAD C6 N6 SING N N 35 XAD C6 N1 DOUB Y N 36 XAD N6 HN61 SING N N 37 XAD N6 HN62 SING N N 38 XAD N1 C2 SING Y N 39 XAD C2 N3 DOUB Y N 40 XAD C2 H2 SING N N 41 # # 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 XAD SMILES ACDLabs 10.04 "O=P(O)(O)OCC3OC(n1cnc2c(ncnc12)N)CCC3O" XAD SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2n(cnc12)[C@H]3CC[C@H](O)[C@@H](CO[P](O)(O)=O)O3" XAD SMILES CACTVS 3.341 "Nc1ncnc2n(cnc12)[CH]3CC[CH](O)[CH](CO[P](O)(O)=O)O3" XAD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@H]3CC[C@@H]([C@H](O3)COP(=O)(O)O)O)N" XAD SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3CCC(C(O3)COP(=O)(O)O)O)N" XAD InChI InChI 1.03 "InChI=1S/C11H16N5O6P/c12-10-9-11(14-4-13-10)16(5-15-9)8-2-1-6(17)7(22-8)3-21-23(18,19)20/h4-8,17H,1-3H2,(H2,12,13,14)(H2,18,19,20)/t6-,7+,8+/m0/s1" XAD InChIKey InChI 1.03 NNMDAQXJNWKVBU-XLPZGREQSA-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 XAD "SYSTEMATIC NAME" ACDLabs 10.04 "9-(2,3-dideoxy-6-O-phosphono-beta-D-erythro-hexopyranosyl)-9H-purin-6-amine" XAD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,6R)-6-(6-aminopurin-9-yl)-3-hydroxy-oxan-2-yl]methyl dihydrogen 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 XAD "Create component" 2006-06-20 RCSB XAD "Modify descriptor" 2011-06-04 RCSB XAD "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id XAD _pdbx_chem_comp_synonyms.name "2',3'-DI-DEOXY-BETA-D-GLUCOPYRANOSYL ADENINE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##