data_9O4 # _chem_comp.id 9O4 _chem_comp.name "(3R,5R)-5-(6-amino-9H-purin-9-yl)oxolan-3-yl dihydrogen phosphate" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H12 N5 O5 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-05-19 _chem_comp.pdbx_modified_date 2017-12-01 _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 301.196 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 9O4 _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 5VU7 _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 9O4 C2 C1 C 0 1 Y N N 16.560 15.496 305.785 4.013 -1.876 -1.061 C2 9O4 1 9O4 C4 C2 C 0 1 Y N N 14.396 14.670 306.401 2.659 -0.145 -0.392 C4 9O4 2 9O4 C5 C3 C 0 1 Y N N 14.258 16.156 306.686 3.667 0.291 0.485 C5 9O4 3 9O4 C6 C4 C 0 1 Y N N 15.074 16.974 306.534 4.866 -0.440 0.532 C6 9O4 4 9O4 "C1'" C5 C 0 1 N N R 12.714 12.857 306.692 0.335 0.693 -0.944 "C1'" 9O4 5 9O4 "C2'" C6 C 0 1 N N N 11.599 12.577 307.601 -0.654 -0.259 -0.225 "C2'" 9O4 6 9O4 "C3'" C7 C 0 1 N N R 10.431 12.431 306.782 -2.026 0.297 -0.677 "C3'" 9O4 7 9O4 "C4'" C8 C 0 1 N N N 10.849 12.220 305.328 -1.722 1.742 -1.116 "C4'" 9O4 8 9O4 C8 C9 C 0 1 Y N N 12.339 15.140 307.187 1.995 1.656 0.695 C8 9O4 9 9O4 N1 N1 N 0 1 Y N N 16.101 16.700 306.134 4.990 -1.506 -0.253 N1 9O4 10 9O4 N3 N2 N 0 1 Y N N 15.719 14.213 305.870 2.874 -1.223 -1.139 N3 9O4 11 9O4 N6 N3 N 0 1 N N N 14.784 18.370 306.856 5.895 -0.060 1.376 N6 9O4 12 9O4 N7 N4 N 0 1 Y N N 12.898 16.219 307.166 3.198 1.393 1.117 N7 9O4 13 9O4 N9 N5 N 0 1 Y N N 13.101 14.246 306.782 1.617 0.735 -0.237 N9 9O4 14 9O4 O1P O1 O 0 1 N N N 7.489 14.851 306.866 -5.298 0.075 -0.758 O1P 9O4 15 9O4 O2P O2 O 0 1 N N N 7.511 12.518 306.237 -4.056 -1.957 0.078 O2P 9O4 16 9O4 "O3'" O3 O 0 1 N N N 9.679 13.639 306.885 -2.952 0.289 0.411 "O3'" 9O4 17 9O4 "O4'" O4 O 0 1 N N N 12.332 12.551 305.295 -0.324 1.976 -0.878 "O4'" 9O4 18 9O4 P P1 P 0 1 N N N 8.257 13.795 306.171 -4.335 -0.535 0.379 P 9O4 19 9O4 O3P O5 O 0 1 N Y N 8.478 14.103 304.617 -5.060 -0.423 1.813 O3P 9O4 20 9O4 H1 H1 H 0 1 N N N 17.575 15.420 305.424 4.157 -2.746 -1.686 H1 9O4 21 9O4 H2 H2 H 0 1 N N N 13.569 12.224 306.971 0.479 0.386 -1.980 H2 9O4 22 9O4 H3 H3 H 0 1 N N N 11.789 11.649 308.160 -0.520 -1.286 -0.563 H3 9O4 23 9O4 H4 H4 H 0 1 N N N 11.466 13.410 308.307 -0.543 -0.190 0.857 H4 9O4 24 9O4 H5 H5 H 0 1 N N N 9.831 11.571 307.115 -2.416 -0.284 -1.513 H5 9O4 25 9O4 H6 H6 H 0 1 N N N 10.288 12.892 304.663 -1.943 1.862 -2.177 H6 9O4 26 9O4 H7 H7 H 0 1 N N N 10.679 11.177 305.024 -2.322 2.441 -0.533 H7 9O4 27 9O4 H8 H8 H 0 1 N N N 11.322 14.980 307.512 1.386 2.481 1.033 H8 9O4 28 9O4 H9 H9 H 0 1 N N N 15.590 18.931 306.665 5.793 0.720 1.944 H9 9O4 29 9O4 H10 H10 H 0 1 N N N 14.017 18.688 306.299 6.718 -0.573 1.399 H10 9O4 30 9O4 H11 H11 H 0 1 N N N 6.681 14.484 307.206 -5.523 1.006 -0.625 H11 9O4 31 9O4 H12 H12 H 0 1 N N N 8.088 13.410 304.098 -5.901 -0.896 1.866 H12 9O4 32 # 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 9O4 "O4'" "C4'" SING N N 1 9O4 "O4'" "C1'" SING N N 2 9O4 "C4'" "C3'" SING N N 3 9O4 C2 N3 DOUB Y N 4 9O4 C2 N1 SING Y N 5 9O4 N3 C4 SING Y N 6 9O4 N1 C6 DOUB Y N 7 9O4 P O2P DOUB N N 8 9O4 P O1P SING N N 9 9O4 P "O3'" SING N N 10 9O4 C4 C5 DOUB Y N 11 9O4 C4 N9 SING Y N 12 9O4 C6 C5 SING Y N 13 9O4 C6 N6 SING N N 14 9O4 C5 N7 SING Y N 15 9O4 "C1'" N9 SING N N 16 9O4 "C1'" "C2'" SING N N 17 9O4 "C3'" "O3'" SING N N 18 9O4 "C3'" "C2'" SING N N 19 9O4 N9 C8 SING Y N 20 9O4 N7 C8 DOUB Y N 21 9O4 P O3P SING N N 22 9O4 C2 H1 SING N N 23 9O4 "C1'" H2 SING N N 24 9O4 "C2'" H3 SING N N 25 9O4 "C2'" H4 SING N N 26 9O4 "C3'" H5 SING N N 27 9O4 "C4'" H6 SING N N 28 9O4 "C4'" H7 SING N N 29 9O4 C8 H8 SING N N 30 9O4 N6 H9 SING N N 31 9O4 N6 H10 SING N N 32 9O4 O1P H11 SING N N 33 9O4 O3P H12 SING N N 34 # 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 9O4 SMILES ACDLabs 12.01 "c3nc1c(ncn1C2CC(OP(O)(=O)O)CO2)c(N)n3" 9O4 InChI InChI 1.03 "InChI=1S/C9H12N5O5P/c10-8-7-9(12-3-11-8)14(4-13-7)6-1-5(2-18-6)19-20(15,16)17/h3-6H,1-2H2,(H2,10,11,12)(H2,15,16,17)/t5-,6-/m1/s1" 9O4 InChIKey InChI 1.03 SRZMSIWIQAVZRP-PHDIDXHHSA-N 9O4 SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@H]3C[C@H](CO3)O[P](O)(O)=O" 9O4 SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3C[CH](CO3)O[P](O)(O)=O" 9O4 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)[C@H]3C[C@H](CO3)OP(=O)(O)O)N" 9O4 SMILES "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)C3CC(CO3)OP(=O)(O)O)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 9O4 "SYSTEMATIC NAME" ACDLabs 12.01 "(3R,5R)-5-(6-amino-9H-purin-9-yl)oxolan-3-yl dihydrogen phosphate" 9O4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(3~{R},5~{R})-5-(6-aminopurin-9-yl)oxolan-3-yl] 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 9O4 "Create component" 2017-05-19 RCSB 9O4 "Initial release" 2017-12-06 RCSB #