data_8XC # _chem_comp.id 8XC _chem_comp.name "4-amino-1-(5-O-phosphono-beta-D-xylofuranosyl)pyrimidin-2(1H)-one" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H14 N3 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-07-16 _chem_comp.pdbx_modified_date 2015-07-24 _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 323.197 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 8XC _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 2N4J _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 8XC P P P 0 1 N N N 78.992 75.769 -20.332 4.169 0.937 0.071 P 8XC 1 8XC OP1 OP1 O 0 1 N N N 78.907 75.742 -21.808 3.923 1.607 -1.226 OP1 8XC 2 8XC OP2 OP2 O 0 1 N N N 77.750 75.874 -19.539 4.612 2.032 1.164 OP2 8XC 3 8XC "O5'" "O5'" O 0 1 N N N 79.805 74.463 -19.840 2.822 0.205 0.560 "O5'" 8XC 4 8XC "C5'" "C5'" C 0 1 N N N 80.778 74.583 -18.803 2.118 -0.747 -0.241 "C5'" 8XC 5 8XC "C4'" "C4'" C 0 1 N N R 82.159 74.133 -19.262 0.888 -1.245 0.522 "C4'" 8XC 6 8XC "O4'" "O4'" O 0 1 N N N 83.170 74.821 -18.531 -0.096 -0.193 0.632 "O4'" 8XC 7 8XC "C1'" "C1'" C 0 1 N N R 84.039 73.857 -17.951 -1.346 -0.868 0.894 "C1'" 8XC 8 8XC N1 N1 N 0 1 N N N 83.769 73.731 -16.500 -2.475 -0.001 0.548 N1 8XC 9 8XC C6 C6 C 0 1 N N N 82.790 74.476 -15.904 -3.448 0.245 1.470 C6 8XC 10 8XC C2 C2 C 0 1 N N N 84.550 72.850 -15.771 -2.543 0.553 -0.677 C2 8XC 11 8XC O2 O2 O 0 1 N N N 85.416 72.178 -16.327 -1.661 0.325 -1.488 O2 8XC 12 8XC N3 N3 N 0 1 N N N 84.325 72.744 -14.433 -3.558 1.345 -1.018 N3 8XC 13 8XC C4 C4 C 0 1 N N N 83.374 73.468 -13.834 -4.531 1.608 -0.155 C4 8XC 14 8XC N4 N4 N 0 1 N N N 83.191 73.343 -12.523 -5.574 2.428 -0.518 N4 8XC 15 8XC C5 C5 C 0 1 N N N 82.561 74.376 -14.580 -4.486 1.048 1.138 C5 8XC 16 8XC "C2'" "C2'" C 0 1 N N R 83.811 72.532 -18.676 -1.322 -2.112 -0.022 "C2'" 8XC 17 8XC "O2'" "O2'" O 0 1 N N N 84.644 72.417 -19.838 -1.919 -3.230 0.638 "O2'" 8XC 18 8XC "C3'" "C3'" C 0 1 N N R 82.338 72.629 -19.054 0.181 -2.366 -0.272 "C3'" 8XC 19 8XC "O3'" "O3'" O 0 1 N N N 81.502 72.139 -17.996 0.482 -2.259 -1.665 "O3'" 8XC 20 8XC O1 O1 O 0 1 N Y N 79.990 76.962 -19.893 5.340 -0.154 -0.102 O1 8XC 21 8XC H1 H1 H 0 1 N N N 77.003 75.913 -20.124 5.419 2.514 0.934 H1 8XC 22 8XC "H5''" "H5''" H 0 0 N N N 80.834 75.636 -18.488 1.801 -0.275 -1.171 "H5''" 8XC 23 8XC "H5'" "H5'" H 0 1 N N N 80.467 73.961 -17.950 2.772 -1.589 -0.465 "H5'" 8XC 24 8XC "H4'" "H4'" H 0 1 N N N 82.259 74.351 -20.335 1.175 -1.603 1.510 "H4'" 8XC 25 8XC "H1'" "H1'" H 0 1 N N N 85.086 74.160 -18.098 -1.404 -1.166 1.941 "H1'" 8XC 26 8XC H6 H6 H 0 1 N N N 82.194 75.151 -16.500 -3.391 -0.196 2.454 H6 8XC 27 8XC H41 H41 H 0 1 N N N 83.762 72.713 -11.996 -5.601 2.815 -1.407 H41 8XC 28 8XC H42 H42 H 0 1 N N N 82.483 73.879 -12.064 -6.284 2.619 0.115 H42 8XC 29 8XC H5 H5 H 0 1 N N N 81.791 74.961 -14.100 -5.268 1.257 1.854 H5 8XC 30 8XC "H2'" "H2'" H 0 1 N N N 83.969 71.692 -17.984 -1.836 -1.905 -0.961 "H2'" 8XC 31 8XC "HO2'" "HO2'" H 0 0 N N N 85.554 72.359 -19.571 -1.931 -4.039 0.108 "HO2'" 8XC 32 8XC "H3'" "H3'" H 0 1 N N N 82.152 72.092 -19.996 0.472 -3.345 0.108 "H3'" 8XC 33 8XC "HO3'" "HO3'" H 0 0 N N N 81.637 71.204 -17.893 0.063 -2.938 -2.211 "HO3'" 8XC 34 8XC H2 H2 H 0 1 N N N 80.318 77.402 -20.668 5.555 -0.632 0.710 H2 8XC 35 # 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 8XC OP1 P DOUB N N 1 8XC P "O5'" SING N N 2 8XC P OP2 SING N N 3 8XC "O5'" "C5'" SING N N 4 8XC "O2'" "C2'" SING N N 5 8XC "C4'" "C3'" SING N N 6 8XC "C4'" "C5'" SING N N 7 8XC "C4'" "O4'" SING N N 8 8XC "C3'" "C2'" SING N N 9 8XC "C3'" "O3'" SING N N 10 8XC "C2'" "C1'" SING N N 11 8XC "O4'" "C1'" SING N N 12 8XC "C1'" N1 SING N N 13 8XC N1 C6 SING N N 14 8XC N1 C2 SING N N 15 8XC O2 C2 DOUB N N 16 8XC C6 C5 DOUB N N 17 8XC C2 N3 SING N N 18 8XC C5 C4 SING N N 19 8XC N3 C4 DOUB N N 20 8XC C4 N4 SING N N 21 8XC P O1 SING N N 22 8XC OP2 H1 SING N N 23 8XC "C5'" "H5''" SING N N 24 8XC "C5'" "H5'" SING N N 25 8XC "C4'" "H4'" SING N N 26 8XC "C1'" "H1'" SING N N 27 8XC C6 H6 SING N N 28 8XC N4 H41 SING N N 29 8XC N4 H42 SING N N 30 8XC C5 H5 SING N N 31 8XC "C2'" "H2'" SING N N 32 8XC "O2'" "HO2'" SING N N 33 8XC "C3'" "H3'" SING N N 34 8XC "O3'" "HO3'" SING N N 35 8XC O1 H2 SING N N 36 # 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 8XC SMILES ACDLabs 12.01 "P(OCC1C(C(C(O1)N2C=CC(=NC2=O)N)O)O)(O)(O)=O" 8XC InChI InChI 1.03 "InChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6+,7-,8-/m1/s1" 8XC InChIKey InChI 1.03 IERHLVCPSMICTF-PXBUCIJWSA-N 8XC SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@H](O)[C@H]2O" 8XC SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O" 8XC SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@H]([C@H](O2)COP(=O)(O)O)O)O" 8XC SMILES "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)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 8XC "SYSTEMATIC NAME" ACDLabs 12.01 "4-amino-1-(5-O-phosphono-beta-D-xylofuranosyl)pyrimidin-2(1H)-one" 8XC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3R,4R,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)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 8XC "Create component" 2015-07-16 RCSB 8XC "Initial release" 2015-07-29 RCSB #