data_A6C # _chem_comp.id A6C _chem_comp.name "2-(4-amino-2-oxopyrimidin-1(2H)-yl)-1,5-anhydro-2-deoxy-6-O-phosphono-D-altritol" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H16 N3 O8 P" _chem_comp.mon_nstd_parent_comp_id C _chem_comp.pdbx_synonyms "((2R,3S,4S,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydro-2H-pyran-2-yl)methyl dihydrogen phosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-08-26 _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 337.223 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A6C _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 3OK2 _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 A6C P P P 0 1 N N N -0.737 3.176 -36.736 4.255 0.743 -0.058 P A6C 1 A6C N1 N1 N 0 1 N N N 4.213 3.844 -34.003 -2.569 -0.041 0.581 N1 A6C 2 A6C C2 C2 C 0 1 N N N 5.268 3.242 -33.257 -3.673 -0.050 -0.189 C2 A6C 3 A6C O2 O2 O 0 1 N N N 6.262 3.952 -32.985 -4.183 -1.115 -0.494 O2 A6C 4 A6C N3 N3 N 0 1 N N N 5.219 1.880 -32.984 -4.219 1.085 -0.622 N3 A6C 5 A6C C4 C4 C 0 1 N N N 4.134 1.149 -33.349 -3.685 2.257 -0.305 C4 A6C 6 A6C N4 N4 N 0 1 N N N 4.087 -0.143 -32.976 -4.258 3.423 -0.758 N4 A6C 7 A6C C5 C5 C 0 1 N N N 3.022 1.765 -34.055 -2.528 2.302 0.499 C5 A6C 8 A6C C6 C6 C 0 1 N N N 3.119 3.085 -34.399 -1.985 1.139 0.932 C6 A6C 9 A6C "C1'" "C1'" C 0 1 N N R 4.354 5.317 -34.376 -1.995 -1.305 1.047 "C1'" A6C 10 A6C "C2'" "C2'" C 0 1 N N S 4.664 5.499 -35.883 -1.512 -2.123 -0.155 "C2'" A6C 11 A6C "O2'" "O2'" O 0 1 N N N 5.031 6.871 -36.037 -1.014 -3.385 0.295 "O2'" A6C 12 A6C "C3'" "C3'" C 0 1 N N S 3.453 5.157 -36.746 -0.396 -1.353 -0.866 "C3'" A6C 13 A6C "O3'" "O3'" O 0 1 N N N 3.630 5.203 -38.152 0.112 -2.138 -1.947 "O3'" A6C 14 A6C "C4'" "C4'" C 0 1 N N R 2.171 5.882 -36.301 0.730 -1.065 0.130 "C4'" A6C 15 A6C "O4'" "O4'" O 0 1 N N N 2.002 5.720 -34.898 0.207 -0.329 1.238 "O4'" A6C 16 A6C "C5'" "C5'" C 0 1 N N N 0.902 5.307 -36.944 1.822 -0.243 -0.558 "C5'" A6C 17 A6C "O5'" "O5'" O 0 1 N N N 0.706 3.927 -36.631 2.924 -0.074 0.336 "O5'" A6C 18 A6C "C6'" "C6'" C 0 1 N N N 3.113 6.141 -34.090 -0.808 -1.019 1.970 "C6'" A6C 19 A6C OP1 OP1 O 0 1 N N N -1.280 3.404 -38.098 3.885 2.104 -0.504 OP1 A6C 20 A6C OP2 OP2 O 0 1 N N N -0.537 1.855 -36.147 5.223 0.842 1.225 OP2 A6C 21 A6C OP3 OP3 O 0 1 N Y N -1.698 3.929 -35.711 5.021 -0.023 -1.250 OP3 A6C 22 A6C HN4 HN4 H 0 1 N N N 4.837 -0.538 -32.446 -5.054 3.390 -1.311 HN4 A6C 23 A6C HN4A HN4A H 0 0 N N N 3.302 -0.708 -33.229 -3.865 4.279 -0.525 HN4A A6C 24 A6C H5 H5 H 0 1 N N N 2.140 1.193 -34.302 -2.081 3.248 0.766 H5 A6C 25 A6C H6 H6 H 0 1 N N N 2.336 3.543 -34.985 -1.099 1.147 1.550 H6 A6C 26 A6C "H1'" "H1'" H 0 1 N N N 5.183 5.672 -33.746 -2.752 -1.870 1.592 "H1'" A6C 27 A6C "H2'" "H2'" H 0 1 N N N 5.468 4.824 -36.210 -2.342 -2.283 -0.844 "H2'" A6C 28 A6C "HO2'" "HO2'" H 0 0 N N N 5.234 7.044 -36.949 -0.691 -3.955 -0.416 "HO2'" A6C 29 A6C "H3'" "H3'" H 0 1 N N N 3.327 4.083 -36.544 -0.790 -0.413 -1.252 "H3'" A6C 30 A6C "HO3'" "HO3'" H 0 0 N Y N 2.815 4.973 -38.582 0.824 -1.711 -2.443 "HO3'" A6C 31 A6C "H4'" "H4'" H 0 1 N N N 2.294 6.932 -36.605 1.151 -2.005 0.485 "H4'" A6C 32 A6C "H5'" "H5'" H 0 1 N N N 0.036 5.875 -36.573 2.159 -0.765 -1.454 "H5'" A6C 33 A6C "H5'A" "H5'A" H 0 0 N N N 0.989 5.407 -38.036 1.424 0.733 -0.833 "H5'A" A6C 34 A6C "H6'" "H6'" H 0 1 N N N 2.845 6.022 -33.030 -1.137 -0.401 2.805 "H6'" A6C 35 A6C "H6'A" "H6'A" H 0 0 N N N 3.331 7.197 -34.309 -0.407 -1.959 2.349 "H6'A" A6C 36 A6C HOP2 HOP2 H 0 0 N N N -0.806 1.187 -36.767 6.046 1.322 1.060 HOP2 A6C 37 A6C HOP3 HOP3 H 0 0 N Y N -2.400 4.354 -36.189 5.294 -0.923 -1.027 HOP3 A6C 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 A6C OP1 P DOUB N N 1 A6C P "O5'" SING N N 2 A6C P OP2 SING N N 3 A6C P OP3 SING N N 4 A6C C6 N1 SING N N 5 A6C "C1'" N1 SING N N 6 A6C N1 C2 SING N N 7 A6C C2 O2 DOUB N N 8 A6C C2 N3 SING N N 9 A6C C4 N3 DOUB N N 10 A6C C5 C4 SING N N 11 A6C C4 N4 SING N N 12 A6C N4 HN4 SING N N 13 A6C N4 HN4A SING N N 14 A6C C6 C5 DOUB N N 15 A6C C5 H5 SING N N 16 A6C C6 H6 SING N N 17 A6C "C2'" "C1'" SING N N 18 A6C "C1'" "C6'" SING N N 19 A6C "C1'" "H1'" SING N N 20 A6C "C3'" "C2'" SING N N 21 A6C "O2'" "C2'" SING N N 22 A6C "C2'" "H2'" SING N N 23 A6C "O2'" "HO2'" SING N N 24 A6C "O3'" "C3'" SING N N 25 A6C "C3'" "C4'" SING N N 26 A6C "C3'" "H3'" SING N N 27 A6C "O3'" "HO3'" SING N N 28 A6C "C5'" "C4'" SING N N 29 A6C "C4'" "O4'" SING N N 30 A6C "C4'" "H4'" SING N N 31 A6C "O4'" "C6'" SING N N 32 A6C "C5'" "O5'" SING N N 33 A6C "C5'" "H5'" SING N N 34 A6C "C5'" "H5'A" SING N N 35 A6C "C6'" "H6'" SING N N 36 A6C "C6'" "H6'A" SING N N 37 A6C OP2 HOP2 SING N N 38 A6C OP3 HOP3 SING N N 39 # # 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 A6C SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OCC(N1C(=O)N=C(N)C=C1)C(O)C2O" A6C SMILES_CANONICAL CACTVS 3.370 "NC1=NC(=O)N(C=C1)[C@@H]2CO[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O" A6C SMILES CACTVS 3.370 "NC1=NC(=O)N(C=C1)[CH]2CO[CH](CO[P](O)(O)=O)[CH](O)[CH]2O" A6C SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C1[C@H]([C@@H]([C@@H]([C@H](O1)COP(=O)(O)O)O)O)N2C=CC(=NC2=O)N" A6C SMILES "OpenEye OEToolkits" 1.7.0 "C1C(C(C(C(O1)COP(=O)(O)O)O)O)N2C=CC(=NC2=O)N" A6C InChI InChI 1.03 "InChI=1S/C10H16N3O8P/c11-7-1-2-13(10(16)12-7)5-3-20-6(9(15)8(5)14)4-21-22(17,18)19/h1-2,5-6,8-9,14-15H,3-4H2,(H2,11,12,16)(H2,17,18,19)/t5-,6-,8+,9-/m1/s1" A6C InChIKey InChI 1.03 VRGYQABDDBPVLA-MTSNSDSCSA-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 A6C "SYSTEMATIC NAME" ACDLabs 12.01 "2-(4-amino-2-oxopyrimidin-1(2H)-yl)-1,5-anhydro-2-deoxy-6-O-phosphono-D-altritol" A6C "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[(2R,3S,4S,5R)-5-(4-azanyl-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-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 A6C "Create component" 2010-08-26 RCSB A6C "Modify descriptor" 2011-06-04 RCSB A6C "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id A6C _pdbx_chem_comp_synonyms.name "((2R,3S,4S,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydro-2H-pyran-2-yl)methyl dihydrogen phosphate" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##