data_XGU # _chem_comp.id XGU _chem_comp.name "2-AMINO-9-(2,3-DIDEOXY-6-O-PHOSPHONO-BETA-D-ERYTHRO-HEXOPYRANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H16 N5 O7 P" _chem_comp.mon_nstd_parent_comp_id DG _chem_comp.pdbx_synonyms "2',3'-DI-DEOXY-BETA-D-GLUCOPYRANOSYL GUANINE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2006-06-20 _chem_comp.pdbx_modified_date 2021-03-13 _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 361.248 _chem_comp.one_letter_code G _chem_comp.three_letter_code XGU _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 XGU OP3 O3P O 0 1 N Y N 9.708 8.606 17.067 4.757 -1.725 1.100 OP3 XGU 1 XGU P P P 0 1 N N N 10.525 7.581 17.948 4.593 -1.278 -0.438 P XGU 2 XGU OP1 O1P O 0 1 N N N 9.679 7.059 19.042 5.627 -0.275 -0.774 OP1 XGU 3 XGU OP2 O2P O 0 1 N N N 11.120 6.573 17.035 4.763 -2.565 -1.391 OP2 XGU 4 XGU "O6'" "O6'" O 0 1 N N N 11.749 8.357 18.646 3.132 -0.637 -0.658 "O6'" XGU 5 XGU "C6'" "C6'" C 0 1 N N N 12.883 8.696 17.863 3.085 0.560 0.121 "C6'" XGU 6 XGU "C5'" "C5'" C 0 1 N N R 13.903 9.433 18.722 1.716 1.222 -0.044 "C5'" XGU 7 XGU "O5'" "O5'" O 0 1 N N N 13.243 10.432 19.523 0.710 0.370 0.501 "O5'" XGU 8 XGU "C4'" "C4'" C 0 1 N N S 14.649 8.519 19.686 1.709 2.565 0.689 "C4'" XGU 9 XGU "O4'" "O4'" O 0 1 N N N 15.298 7.480 18.965 2.736 3.406 0.159 "O4'" XGU 10 XGU "C3'" "C3'" C 0 1 N N N 15.667 9.334 20.498 0.344 3.235 0.491 "C3'" XGU 11 XGU "C2'" "C2'" C 0 1 N N N 14.996 10.555 21.162 -0.751 2.252 0.919 "C2'" XGU 12 XGU "C1'" "C1'" C 0 1 N N R 14.155 11.315 20.143 -0.558 0.933 0.169 "C1'" XGU 13 XGU N9 N9 N 0 1 Y N N 13.320 12.330 20.736 -1.620 -0.003 0.547 N9 XGU 14 XGU C8 C8 C 0 1 Y N N 13.143 12.604 22.085 -1.544 -0.962 1.516 C8 XGU 15 XGU N7 N7 N 0 1 Y N N 12.216 13.519 22.199 -2.670 -1.610 1.584 N7 XGU 16 XGU C4 C4 C 0 1 Y N N 12.487 13.124 20.017 -2.870 -0.075 -0.006 C4 XGU 17 XGU C5 C5 C 0 1 Y N N 11.805 13.901 20.934 -3.533 -1.109 0.666 C5 XGU 18 XGU N3 N3 N 0 1 N N N 12.278 13.246 18.664 -3.502 0.598 -0.974 N3 XGU 19 XGU C2 C2 C 0 1 N N N 11.395 14.124 18.217 -4.739 0.306 -1.308 C2 XGU 20 XGU N2 N2 N 0 1 N N N 11.163 14.218 16.897 -5.347 1.024 -2.308 N2 XGU 21 XGU N1 N1 N 0 1 N N N 10.652 14.905 19.097 -5.438 -0.685 -0.687 N1 XGU 22 XGU C6 C6 C 0 1 N N N 10.853 14.821 20.477 -4.864 -1.412 0.297 C6 XGU 23 XGU O6 O6 O 0 1 N N N 10.151 15.509 21.296 -5.479 -2.304 0.856 O6 XGU 24 XGU HOP3 3HOP H 0 0 N N N 9.544 9.396 17.569 4.066 -2.377 1.277 HOP3 XGU 25 XGU HOP2 2HOP H 0 0 N N N 11.247 6.959 16.176 5.649 -2.917 -1.229 HOP2 XGU 26 XGU "H6'1" "1H6'" H 0 0 N N N 12.570 9.347 17.033 3.863 1.244 -0.218 "H6'1" XGU 27 XGU "H6'2" "2H6'" H 0 0 N N N 13.338 7.777 17.464 3.247 0.317 1.171 "H6'2" XGU 28 XGU "H5'" "H5'" H 0 1 N N N 14.623 9.873 18.017 1.518 1.386 -1.103 "H5'" XGU 29 XGU "H4'" "H4'" H 0 1 N N N 13.931 8.063 20.383 1.884 2.402 1.752 "H4'" XGU 30 XGU "H4T'" "H4T'" H 0 0 N N N 15.443 7.759 18.068 2.690 4.242 0.644 "H4T'" XGU 31 XGU "H3'1" "1H3'" H 0 0 N N N 16.453 9.693 19.817 0.213 3.494 -0.560 "H3'1" XGU 32 XGU "H3'2" "2H3'" H 0 0 N N N 16.095 8.692 21.282 0.287 4.136 1.102 "H3'2" XGU 33 XGU "H2'1" "1H2'" H 0 0 N N N 15.776 11.224 21.553 -1.729 2.669 0.678 "H2'1" XGU 34 XGU "H2'2" "2H2'" H 0 0 N N N 14.348 10.211 21.981 -0.683 2.075 1.992 "H2'2" XGU 35 XGU "H1'" "H1'" H 0 1 N N N 14.881 11.768 19.452 -0.603 1.116 -0.905 "H1'" XGU 36 XGU H8 H8 H 0 1 N N N 13.679 12.141 22.900 -0.679 -1.153 2.133 H8 XGU 37 XGU HN21 1HN2 H 0 0 N N N 11.615 13.664 16.198 -4.863 1.735 -2.757 HN21 XGU 38 XGU HN22 2HN2 H 0 0 N N N 10.475 14.920 16.712 -6.258 0.818 -2.568 HN22 XGU 39 XGU HN1 HN1 H 0 1 N N N 9.964 15.535 18.737 -6.350 -0.875 -0.957 HN1 XGU 40 # # 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 XGU OP3 P SING N N 1 XGU OP3 HOP3 SING N N 2 XGU P OP1 DOUB N N 3 XGU P OP2 SING N N 4 XGU P "O6'" SING N N 5 XGU OP2 HOP2 SING N N 6 XGU "O6'" "C6'" SING N N 7 XGU "C6'" "C5'" SING N N 8 XGU "C6'" "H6'1" SING N N 9 XGU "C6'" "H6'2" SING N N 10 XGU "C5'" "O5'" SING N N 11 XGU "C5'" "C4'" SING N N 12 XGU "C5'" "H5'" SING N N 13 XGU "O5'" "C1'" SING N N 14 XGU "C4'" "O4'" SING N N 15 XGU "C4'" "C3'" SING N N 16 XGU "C4'" "H4'" SING N N 17 XGU "O4'" "H4T'" SING N N 18 XGU "C3'" "C2'" SING N N 19 XGU "C3'" "H3'1" SING N N 20 XGU "C3'" "H3'2" SING N N 21 XGU "C2'" "C1'" SING N N 22 XGU "C2'" "H2'1" SING N N 23 XGU "C2'" "H2'2" SING N N 24 XGU "C1'" N9 SING N N 25 XGU "C1'" "H1'" SING N N 26 XGU N9 C8 SING Y N 27 XGU N9 C4 SING Y N 28 XGU C8 N7 DOUB Y N 29 XGU C8 H8 SING N N 30 XGU N7 C5 SING Y N 31 XGU C4 C5 DOUB Y N 32 XGU C4 N3 SING N N 33 XGU C5 C6 SING N N 34 XGU N3 C2 DOUB N N 35 XGU C2 N2 SING N N 36 XGU C2 N1 SING N N 37 XGU N2 HN21 SING N N 38 XGU N2 HN22 SING N N 39 XGU N1 C6 SING N N 40 XGU N1 HN1 SING N N 41 XGU C6 O6 DOUB N N 42 # # 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 XGU SMILES ACDLabs 10.04 "O=C2NC(=Nc1n(cnc12)C3OC(C(O)CC3)COP(=O)(O)O)N" XGU SMILES_CANONICAL CACTVS 3.341 "NC1=Nc2n(cnc2C(=O)N1)[C@H]3CC[C@H](O)[C@@H](CO[P](O)(O)=O)O3" XGU SMILES CACTVS 3.341 "NC1=Nc2n(cnc2C(=O)N1)[CH]3CC[CH](O)[CH](CO[P](O)(O)=O)O3" XGU SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1[C@H]3CC[C@@H]([C@H](O3)COP(=O)(O)O)O)N=C(NC2=O)N" XGU SMILES "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1C3CCC(C(O3)COP(=O)(O)O)O)N=C(NC2=O)N" XGU InChI InChI 1.03 "InChI=1S/C11H16N5O7P/c12-11-14-9-8(10(18)15-11)13-4-16(9)7-2-1-5(17)6(23-7)3-22-24(19,20)21/h4-7,17H,1-3H2,(H2,19,20,21)(H3,12,14,15,18)/t5-,6+,7+/m0/s1" XGU InChIKey InChI 1.03 AHHGXXBXJPSOJX-RRKCRQDMSA-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 XGU "SYSTEMATIC NAME" ACDLabs 10.04 "2-amino-9-(2,3-dideoxy-6-O-phosphono-beta-D-erythro-hexopyranosyl)-1,9-dihydro-6H-purin-6-one" XGU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,6R)-6-(2-amino-6-oxo-1H-purin-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 XGU "Create component" 2006-06-20 RCSB XGU "Modify descriptor" 2011-06-04 RCSB XGU "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id XGU _pdbx_chem_comp_synonyms.name "2',3'-DI-DEOXY-BETA-D-GLUCOPYRANOSYL GUANINE" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##