data_XMP # _chem_comp.id XMP _chem_comp.name "XANTHOSINE-5'-MONOPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H14 N4 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE" _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 1999-07-12 _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 365.213 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XMP _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 1QK5 _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 XMP P P P 0 1 N N N 26.094 44.979 61.192 5.080 0.916 0.179 P XMP 1 XMP O1P O1P O 0 1 N N N 25.219 46.179 61.310 5.464 1.919 1.379 O1P XMP 2 XMP O2P O2P O 0 1 N N N 27.503 45.102 60.830 6.254 -0.170 -0.009 O2P XMP 3 XMP "O5'" "O5'" O 0 1 N N N 25.411 43.920 60.198 3.702 0.162 0.531 "O5'" XMP 4 XMP O3P O3P O 0 1 N N N 25.957 44.296 62.525 4.916 1.686 -1.074 O3P XMP 5 XMP "C5'" "C5'" C 0 1 N N N 24.030 44.158 59.982 3.041 -0.718 -0.381 "C5'" XMP 6 XMP "C4'" "C4'" C 0 1 N N R 23.192 42.953 60.249 1.766 -1.261 0.267 "C4'" XMP 7 XMP "O4'" "O4'" O 0 1 N N N 22.052 42.947 59.349 0.824 -0.193 0.462 "O4'" XMP 8 XMP "C1'" "C1'" C 0 1 N N R 22.490 42.199 58.205 -0.493 -0.754 0.278 "C1'" XMP 9 XMP N9 N9 N 0 1 Y N N 22.375 43.187 57.149 -1.461 0.297 -0.045 N9 XMP 10 XMP C4 C4 C 0 1 Y N N 21.623 43.108 56.018 -2.805 0.239 0.150 C4 XMP 11 XMP N3 N3 N 0 1 N N N 20.848 42.083 55.667 -3.664 -0.707 0.662 N3 XMP 12 XMP N1 N1 N 0 1 N N N 20.380 43.408 53.812 -5.532 0.682 0.309 N1 XMP 13 XMP C2 C2 C 0 1 N N N 20.210 42.244 54.501 -4.986 -0.471 0.730 C2 XMP 14 XMP O2 O2 O 0 1 N N N 19.456 41.368 54.083 -5.712 -1.332 1.188 O2 XMP 15 XMP C6 C6 C 0 1 N N N 21.187 44.492 54.152 -4.764 1.666 -0.206 C6 XMP 16 XMP O6 O6 O 0 1 N N N 21.223 45.473 53.409 -5.262 2.710 -0.587 O6 XMP 17 XMP C5 C5 C 0 1 Y N N 21.831 44.314 55.369 -3.319 1.449 -0.298 C5 XMP 18 XMP N7 N7 N 1 1 Y N N 22.714 45.112 56.087 -2.278 2.191 -0.746 N7 XMP 19 XMP C8 C8 C 0 1 Y N N 22.999 44.402 57.145 -1.176 1.514 -0.592 C8 XMP 20 XMP "C2'" "C2'" C 0 1 N N R 23.918 41.745 58.500 -0.311 -1.717 -0.923 "C2'" XMP 21 XMP "O2'" "O2'" O 0 1 N N N 24.205 40.545 57.868 -1.295 -2.753 -0.900 "O2'" XMP 22 XMP "C3'" "C3'" C 0 1 N N S 23.778 41.576 59.994 1.103 -2.292 -0.667 "C3'" XMP 23 XMP "O3'" "O3'" O 0 1 N N N 22.857 40.513 60.415 1.016 -3.565 -0.024 "O3'" XMP 24 XMP HOP1 HOP1 H 0 0 N N N 25.033 46.347 62.226 6.286 2.408 1.235 HOP1 XMP 25 XMP HOP2 HOP2 H 0 0 N N N 27.586 45.129 59.884 6.417 -0.712 0.775 HOP2 XMP 26 XMP "H5'2" "H5'2" H 0 0 N N N 23.706 44.964 60.657 2.784 -0.172 -1.289 "H5'2" XMP 27 XMP "H5'1" "H5'1" H 0 0 N N N 23.898 44.430 58.924 3.704 -1.546 -0.631 "H5'1" XMP 28 XMP "H4'" "H4'" H 0 1 N N N 23.010 43.068 61.328 2.006 -1.724 1.224 "H4'" XMP 29 XMP "H1'" "H1'" H 0 1 N N N 21.935 41.287 57.941 -0.805 -1.301 1.168 "H1'" XMP 30 XMP H3 H3 H 0 1 N N N 20.751 41.261 56.228 -3.311 -1.554 0.976 H3 XMP 31 XMP H1 H1 H 0 1 N N N 19.863 43.494 52.960 -6.491 0.809 0.377 H1 XMP 32 XMP H7 H7 H 0 1 N N N 23.053 46.022 55.848 -2.342 3.084 -1.118 H7 XMP 33 XMP H8 H8 H 0 1 N N N 23.657 44.739 57.932 -0.189 1.862 -0.860 H8 XMP 34 XMP "H2'" "H2'" H 0 1 N N N 24.725 42.414 58.165 -0.345 -1.172 -1.867 "H2'" XMP 35 XMP H2O1 H2O1 H 0 0 N N N 24.271 40.688 56.931 -1.223 -3.381 -1.632 H2O1 XMP 36 XMP "H3'" "H3'" H 0 1 N N N 24.695 41.282 60.526 1.657 -2.373 -1.602 "H3'" XMP 37 XMP H3O1 H3O1 H 0 0 N N N 22.658 39.954 59.673 0.606 -4.253 -0.566 H3O1 XMP 38 # # 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 XMP P O1P SING N N 1 XMP P O2P SING N N 2 XMP P "O5'" SING N N 3 XMP P O3P DOUB N N 4 XMP O1P HOP1 SING N N 5 XMP O2P HOP2 SING N N 6 XMP "O5'" "C5'" SING N N 7 XMP "C5'" "C4'" SING N N 8 XMP "C5'" "H5'2" SING N N 9 XMP "C5'" "H5'1" SING N N 10 XMP "C4'" "O4'" SING N N 11 XMP "C4'" "C3'" SING N N 12 XMP "C4'" "H4'" SING N N 13 XMP "O4'" "C1'" SING N N 14 XMP "C1'" N9 SING N N 15 XMP "C1'" "C2'" SING N N 16 XMP "C1'" "H1'" SING N N 17 XMP N9 C4 SING Y N 18 XMP N9 C8 SING Y N 19 XMP C4 N3 SING N N 20 XMP C4 C5 DOUB Y N 21 XMP N3 C2 SING N N 22 XMP N3 H3 SING N N 23 XMP N1 C2 SING N N 24 XMP N1 C6 SING N N 25 XMP N1 H1 SING N N 26 XMP C2 O2 DOUB N N 27 XMP C6 O6 DOUB N N 28 XMP C6 C5 SING N N 29 XMP C5 N7 SING Y N 30 XMP N7 C8 DOUB Y N 31 XMP N7 H7 SING N N 32 XMP C8 H8 SING N N 33 XMP "C2'" "O2'" SING N N 34 XMP "C2'" "C3'" SING N N 35 XMP "C2'" "H2'" SING N N 36 XMP "O2'" H2O1 SING N N 37 XMP "C3'" "O3'" SING N N 38 XMP "C3'" "H3'" SING N N 39 XMP "O3'" H3O1 SING N N 40 # # 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 XMP SMILES ACDLabs 10.04 "O=C3Nc1c([nH+]cn1C2OC(C(O)C2O)COP(=O)(O)O)C(=O)N3" XMP SMILES_CANONICAL CACTVS 3.341 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)n2c[nH+]c3C(=O)NC(=O)Nc23" XMP SMILES CACTVS 3.341 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)n2c[nH+]c3C(=O)NC(=O)Nc23" XMP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1[nH+]c2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)NC(=O)NC2=O" XMP SMILES "OpenEye OEToolkits" 1.5.0 "c1[nH+]c2c(n1C3C(C(C(O3)COP(=O)(O)O)O)O)NC(=O)NC2=O" XMP InChI InChI 1.03 "InChI=1S/C10H13N4O9P/c15-5-3(1-22-24(19,20)21)23-9(6(5)16)14-2-11-4-7(14)12-10(18)13-8(4)17/h2-3,5-6,9,15-16H,1H2,(H2,19,20,21)(H2,12,13,17,18)/p+1/t3-,5-,6-,9-/m1/s1" XMP InChIKey InChI 1.03 DCTLYFZHFGENCW-UUOKFMHZSA-O # # 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 XMP "SYSTEMATIC NAME" ACDLabs 10.04 "5'-xanthylic acid" XMP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(2,6-dioxo-3H-purin-7-ium-9-yl)-3,4-dihydroxy-oxolan-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 XMP "Create component" 1999-07-12 RCSB XMP "Modify descriptor" 2011-06-04 RCSB XMP "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id XMP _pdbx_chem_comp_synonyms.name "5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##