data_A6A # _chem_comp.id A6A _chem_comp.name "2-(6-amino-9H-purin-9-yl)-1,5-anhydro-2-deoxy-6-O-phosphono-D-altritol" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H16 N5 O7 P" _chem_comp.mon_nstd_parent_comp_id A _chem_comp.pdbx_synonyms "((2R,3S,4S,5R)-5-(6-amino-9H-purin-9-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 361.248 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A6A _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 A6A P P P 0 1 N N N -9.601 -0.703 1.990 4.764 0.980 0.120 P A6A 1 A6A N1 N1 N 0 1 Y N N -3.814 5.562 4.836 -5.812 0.992 0.110 N1 A6A 2 A6A C2 C2 C 0 1 Y N N -4.832 6.434 4.861 -5.625 -0.223 0.593 C2 A6A 3 A6A N3 N3 N 0 1 Y N N -6.110 6.230 4.597 -4.430 -0.765 0.701 N3 A6A 4 A6A C4 C4 C 0 1 Y N N -6.323 4.914 4.284 -3.346 -0.095 0.321 C4 A6A 5 A6A C5 C5 C 0 1 Y N N -5.366 3.902 4.230 -3.492 1.202 -0.199 C5 A6A 6 A6A C6 C6 C 0 1 Y N N -4.054 4.249 4.534 -4.788 1.736 -0.295 C6 A6A 7 A6A N6 N6 N 0 1 N N N -3.077 3.345 4.528 -4.994 3.009 -0.799 N6 A6A 8 A6A N7 N7 N 0 1 Y N N -5.914 2.687 3.881 -2.251 1.652 -0.503 N7 A6A 9 A6A C8 C8 C 0 1 Y N N -7.185 2.973 3.709 -1.374 0.736 -0.210 C8 A6A 10 A6A N9 N9 N 0 1 Y N N -7.510 4.281 3.921 -2.000 -0.361 0.302 N9 A6A 11 A6A "C1'" "C1'" C 0 1 N N R -8.872 4.861 3.812 -1.355 -1.598 0.750 "C1'" A6A 12 A6A "C2'" "C2'" C 0 1 N N S -9.345 5.041 2.334 -0.738 -2.318 -0.453 "C2'" A6A 13 A6A "O2'" "O2'" O 0 1 N N N -10.485 5.917 2.327 -0.167 -3.557 -0.027 "O2'" A6A 14 A6A "C3'" "C3'" C 0 1 N N S -9.782 3.758 1.671 0.352 -1.431 -1.062 "C3'" A6A 15 A6A "O3'" "O3'" O 0 1 N N N -10.354 4.004 0.417 0.984 -2.124 -2.140 "O3'" A6A 16 A6A "C4'" "C4'" C 0 1 N N R -10.737 2.955 2.565 1.391 -1.103 0.014 "C4'" A6A 17 A6A "O4'" "O4'" O 0 1 N N N -10.022 2.770 3.760 0.747 -0.462 1.117 "O4'" A6A 18 A6A "C5'" "C5'" C 0 1 N N N -10.966 1.553 2.061 2.452 -0.168 -0.570 "C5'" A6A 19 A6A "O5'" "O5'" O 0 1 N N N -9.722 0.892 2.030 3.483 0.045 0.396 "O5'" A6A 20 A6A "C6'" "C6'" C 0 1 N N N -9.915 4.003 4.480 -0.250 -1.263 1.755 "C6'" A6A 21 A6A OP1 OP1 O 0 1 N N N -10.337 -1.278 0.823 5.452 0.524 -1.108 OP1 A6A 22 A6A OP2 OP2 O 0 1 N N N -8.147 -1.043 2.083 4.285 2.506 -0.069 OP2 A6A 23 A6A OP3 OP3 O 0 1 N Y N -10.424 -1.184 3.297 5.776 0.887 1.368 OP3 A6A 24 A6A H2 H2 H 0 1 N N N -4.570 7.445 5.136 -6.485 -0.794 0.911 H2 A6A 25 A6A HN6 HN6 H 0 1 N N N -2.212 3.786 4.768 -4.238 3.543 -1.091 HN6 A6A 26 A6A HN6A HN6A H 0 0 N N N -3.282 2.629 5.195 -5.893 3.367 -0.860 HN6A A6A 27 A6A H8 H8 H 0 1 N N N -7.915 2.231 3.422 -0.308 0.831 -0.351 H8 A6A 28 A6A "H1'" "H1'" H 0 1 N N N -8.782 5.838 4.309 -2.094 -2.244 1.223 "H1'" A6A 29 A6A "H2'" "H2'" H 0 1 N N N -8.482 5.435 1.778 -1.510 -2.510 -1.198 "H2'" A6A 30 A6A "HO2'" "HO2'" H 0 0 N N N -10.787 6.038 1.434 0.242 -4.067 -0.739 "HO2'" A6A 31 A6A "H3'" "H3'" H 0 1 N N N -8.881 3.146 1.518 -0.094 -0.508 -1.431 "H3'" A6A 32 A6A "HO3'" "HO3'" H 0 0 N Y N -10.620 3.181 0.023 1.687 -1.620 -2.573 "HO3'" A6A 33 A6A "H4'" "H4'" H 0 1 N N N -11.699 3.484 2.630 1.865 -2.023 0.354 "H4'" A6A 34 A6A "H5'" "H5'" H 0 1 N N N -11.657 1.021 2.732 2.881 -0.619 -1.465 "H5'" A6A 35 A6A "H5'A" "H5'A" H 0 0 N N N -11.400 1.583 1.051 1.993 0.786 -0.828 "H5'A" A6A 36 A6A "H6'" "H6'" H 0 1 N N N -9.620 3.802 5.520 -0.677 -0.712 2.594 "H6'" A6A 37 A6A "H6'A" "H6'A" H 0 0 N N N -10.884 4.523 4.473 0.203 -2.186 2.119 "H6'A" A6A 38 A6A HOP2 HOP2 H 0 0 N N N -7.904 -1.598 1.352 3.825 2.872 0.699 HOP2 A6A 39 A6A HOP3 HOP3 H 0 0 N Y N -11.168 -1.709 3.028 6.573 1.426 1.270 HOP3 A6A 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 A6A OP1 P DOUB N N 1 A6A P "O5'" SING N N 2 A6A P OP2 SING N N 3 A6A P OP3 SING N N 4 A6A C6 N1 DOUB Y N 5 A6A N1 C2 SING Y N 6 A6A N3 C2 DOUB Y N 7 A6A C2 H2 SING N N 8 A6A C4 N3 SING Y N 9 A6A N9 C4 SING Y N 10 A6A C5 C4 DOUB Y N 11 A6A N7 C5 SING Y N 12 A6A C5 C6 SING Y N 13 A6A N6 C6 SING N N 14 A6A N6 HN6 SING N N 15 A6A N6 HN6A SING N N 16 A6A C8 N7 DOUB Y N 17 A6A C8 N9 SING Y N 18 A6A C8 H8 SING N N 19 A6A "C1'" N9 SING N N 20 A6A "C2'" "C1'" SING N N 21 A6A "C1'" "C6'" SING N N 22 A6A "C1'" "H1'" SING N N 23 A6A "C3'" "C2'" SING N N 24 A6A "O2'" "C2'" SING N N 25 A6A "C2'" "H2'" SING N N 26 A6A "O2'" "HO2'" SING N N 27 A6A "O3'" "C3'" SING N N 28 A6A "C3'" "C4'" SING N N 29 A6A "C3'" "H3'" SING N N 30 A6A "O3'" "HO3'" SING N N 31 A6A "C5'" "C4'" SING N N 32 A6A "C4'" "O4'" SING N N 33 A6A "C4'" "H4'" SING N N 34 A6A "O4'" "C6'" SING N N 35 A6A "O5'" "C5'" SING N N 36 A6A "C5'" "H5'" SING N N 37 A6A "C5'" "H5'A" SING N N 38 A6A "C6'" "H6'" SING N N 39 A6A "C6'" "H6'A" SING N N 40 A6A OP2 HOP2 SING N N 41 A6A OP3 HOP3 SING 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 A6A SMILES ACDLabs 12.01 "O=P(O)(O)OCC3OCC(n1cnc2c(ncnc12)N)C(O)C3O" A6A SMILES_CANONICAL CACTVS 3.370 "Nc1ncnc2n(cnc12)[C@@H]3CO[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O" A6A SMILES CACTVS 3.370 "Nc1ncnc2n(cnc12)[CH]3CO[CH](CO[P](O)(O)=O)[CH](O)[CH]3O" A6A SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "c1nc(c2c(n1)n(cn2)[C@@H]3CO[C@@H]([C@H]([C@H]3O)O)COP(=O)(O)O)N" A6A SMILES "OpenEye OEToolkits" 1.7.0 "c1nc(c2c(n1)n(cn2)C3COC(C(C3O)O)COP(=O)(O)O)N" A6A InChI InChI 1.03 "InChI=1S/C11H16N5O7P/c12-10-7-11(14-3-13-10)16(4-15-7)5-1-22-6(9(18)8(5)17)2-23-24(19,20)21/h3-6,8-9,17-18H,1-2H2,(H2,12,13,14)(H2,19,20,21)/t5-,6-,8+,9-/m1/s1" A6A InChIKey InChI 1.03 WJZBVGLXFAAYLT-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 A6A "SYSTEMATIC NAME" ACDLabs 12.01 "2-(6-amino-9H-purin-9-yl)-1,5-anhydro-2-deoxy-6-O-phosphono-D-altritol" A6A "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[(2R,3S,4S,5R)-5-(6-aminopurin-9-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 A6A "Create component" 2010-08-26 RCSB A6A "Modify aromatic_flag" 2011-06-04 RCSB A6A "Modify descriptor" 2011-06-04 RCSB A6A "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id A6A _pdbx_chem_comp_synonyms.name "((2R,3S,4S,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydro-2H-pyran-2-yl)methyl dihydrogen phosphate" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##