data_5JO # _chem_comp.id 5JO _chem_comp.name "2'-O-prop-2-yn-1-yladenosine 5'-(dihydrogen phosphate)" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C13 H16 N5 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "2'-Propargyl-Adenosine" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-10-02 _chem_comp.pdbx_modified_date 2020-06-17 _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 385.269 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 5JO _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 5E36 _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 5JO "O5'" O1 O 0 1 N N N 10.293 20.969 -9.088 3.763 -0.285 -0.506 "O5'" 5JO 1 5JO "C5'" C1 C 0 1 N N N 9.041 21.641 -9.281 3.010 0.543 0.383 "C5'" 5JO 2 5JO "C4'" C2 C 0 1 N N R 8.028 21.154 -8.276 1.651 0.861 -0.245 "C4'" 5JO 3 5JO "O4'" O2 O 0 1 N N N 7.731 19.750 -8.505 0.826 -0.324 -0.287 "O4'" 5JO 4 5JO "C3'" C3 C 0 1 N N R 8.449 21.191 -6.812 0.869 1.856 0.640 "C3'" 5JO 5 5JO "O3'" O3 O 0 1 N Y N 8.391 22.516 -6.283 1.007 3.187 0.139 "O3'" 5JO 6 5JO "C2'" C4 C 0 1 N N R 7.442 20.226 -6.202 -0.598 1.384 0.529 "C2'" 5JO 7 5JO "O2'" O4 O 0 1 N N N 6.176 20.840 -6.033 -1.412 2.410 -0.044 "O2'" 5JO 8 5JO "C1'" C5 C 0 1 N N R 7.407 19.128 -7.269 -0.529 0.160 -0.411 "C1'" 5JO 9 5JO N9 N1 N 0 1 Y N N 8.371 18.052 -7.024 -1.479 -0.868 0.021 N9 5JO 10 5JO C8 C6 C 0 1 Y N N 9.653 17.935 -7.502 -1.220 -1.898 0.875 C8 5JO 11 5JO N7 N2 N 0 1 Y N N 10.272 16.853 -7.096 -2.290 -2.621 1.037 N7 5JO 12 5JO C5 C7 C 0 1 Y N N 9.335 16.213 -6.297 -3.301 -2.101 0.299 C5 5JO 13 5JO C6 C8 C 0 1 Y N N 9.375 15.011 -5.570 -4.647 -2.446 0.085 C6 5JO 14 5JO N6 N3 N 0 1 N N N 10.441 14.207 -5.527 -5.203 -3.549 0.709 N6 5JO 15 5JO N1 N4 N 0 1 Y N N 8.274 14.665 -4.869 -5.372 -1.689 -0.731 N1 5JO 16 5JO C2 C9 C 0 1 Y N N 7.206 15.473 -4.912 -4.850 -0.635 -1.331 C2 5JO 17 5JO N3 N5 N 0 1 Y N N 7.048 16.627 -5.557 -3.595 -0.274 -1.160 N3 5JO 18 5JO C4 C10 C 0 1 Y N N 8.162 16.944 -6.240 -2.794 -0.967 -0.357 C4 5JO 19 5JO P P1 P 0 1 N N N 11.537 21.262 -10.036 5.245 -0.815 -0.166 P 5JO 20 5JO OP1 O5 O 0 1 N N N 11.661 22.720 -10.306 6.120 0.336 0.151 OP1 5JO 21 5JO OP2 O6 O 0 1 N N N 12.693 20.534 -9.455 5.183 -1.806 1.101 OP2 5JO 22 5JO "C6'" C11 C 0 1 N N N 5.267 19.976 -5.384 -2.011 3.281 0.917 "C6'" 5JO 23 5JO "C7'" C12 C 0 1 N N N 4.430 20.869 -4.675 -2.823 4.294 0.222 "C7'" 5JO 24 5JO "C8'" C13 C 0 1 N N N 3.649 21.627 -4.054 -3.470 5.101 -0.332 "C8'" 5JO 25 5JO H1 H1 H 0 1 N N N 9.187 22.724 -9.154 2.859 0.020 1.327 H1 5JO 26 5JO H2 H2 H 0 1 N N N 8.672 21.437 -10.297 3.553 1.470 0.563 H2 5JO 27 5JO H3 H3 H 0 1 N N N 7.107 21.745 -8.389 1.784 1.268 -1.248 H3 5JO 28 5JO H4 H4 H 0 1 N N N 9.462 20.775 -6.712 1.213 1.800 1.673 H4 5JO 29 5JO H5 H5 H 0 1 N N N 8.658 22.506 -5.371 1.917 3.512 0.130 H5 5JO 30 5JO H6 H6 H 0 1 N N N 7.829 19.821 -5.255 -0.982 1.096 1.508 H6 5JO 31 5JO H7 H7 H 0 1 N N N 6.391 18.709 -7.310 -0.733 0.457 -1.439 H7 5JO 32 5JO H8 H8 H 0 1 N N N 10.109 18.667 -8.152 -0.268 -2.087 1.347 H8 5JO 33 5JO H9 H9 H 0 1 N N N 10.243 13.421 -4.942 -4.663 -4.094 1.303 H9 5JO 34 5JO H10 H10 H 0 1 N N N 10.656 13.889 -6.450 -6.133 -3.777 0.553 H10 5JO 35 5JO H11 H11 H 0 1 N N N 6.351 15.141 -4.342 -5.475 -0.047 -1.986 H11 5JO 36 5JO H13 H13 H 0 1 N N N 13.414 21.138 -9.322 4.627 -2.585 0.964 H13 5JO 37 5JO H14 H14 H 0 1 N N N 4.690 19.389 -6.114 -2.648 2.701 1.585 H14 5JO 38 5JO H15 H15 H 0 1 N N N 5.791 19.295 -4.697 -1.231 3.775 1.496 H15 5JO 39 5JO H16 H16 H 0 1 N N N 2.988 22.268 -3.529 -4.049 5.824 -0.827 H16 5JO 40 5JO OP3 OP3 O 0 1 N Y N 11.129 20.546 -11.408 5.837 -1.605 -1.438 OP3 5JO 41 5JO H12 H12 H 0 1 N Y N 11.054 21.197 -12.095 6.729 -1.953 -1.304 H12 5JO 42 # # 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 5JO OP1 P DOUB N N 1 5JO P OP2 SING N N 2 5JO P "O5'" SING N N 3 5JO "C5'" "O5'" SING N N 4 5JO "C5'" "C4'" SING N N 5 5JO "O4'" "C4'" SING N N 6 5JO "O4'" "C1'" SING N N 7 5JO "C4'" "C3'" SING N N 8 5JO C8 N7 DOUB Y N 9 5JO C8 N9 SING Y N 10 5JO "C1'" N9 SING N N 11 5JO "C1'" "C2'" SING N N 12 5JO N7 C5 SING Y N 13 5JO N9 C4 SING Y N 14 5JO "C3'" "O3'" SING N N 15 5JO "C3'" "C2'" SING N N 16 5JO C5 C4 DOUB Y N 17 5JO C5 C6 SING Y N 18 5JO C4 N3 SING Y N 19 5JO "C2'" "O2'" SING N N 20 5JO "O2'" "C6'" SING N N 21 5JO C6 N6 SING N N 22 5JO C6 N1 DOUB Y N 23 5JO N3 C2 DOUB Y N 24 5JO "C6'" "C7'" SING N N 25 5JO C2 N1 SING Y N 26 5JO "C7'" "C8'" TRIP N N 27 5JO "C5'" H1 SING N N 28 5JO "C5'" H2 SING N N 29 5JO "C4'" H3 SING N N 30 5JO "C3'" H4 SING N N 31 5JO "O3'" H5 SING N N 32 5JO "C2'" H6 SING N N 33 5JO "C1'" H7 SING N N 34 5JO C8 H8 SING N N 35 5JO N6 H9 SING N N 36 5JO N6 H10 SING N N 37 5JO C2 H11 SING N N 38 5JO OP2 H13 SING N N 39 5JO "C6'" H14 SING N N 40 5JO "C6'" H15 SING N N 41 5JO "C8'" H16 SING N N 42 5JO P OP3 SING N N 43 5JO OP3 H12 SING N N 44 # # 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 5JO SMILES ACDLabs 12.01 "O(CC1C(O)C(OCC#C)C(O1)n2c3c(nc2)c(N)ncn3)P(O)(O)=O" 5JO InChI InChI 1.03 "InChI=1S/C13H16N5O7P/c1-2-3-23-10-9(19)7(4-24-26(20,21)22)25-13(10)18-6-17-8-11(14)15-5-16-12(8)18/h1,5-7,9-10,13,19H,3-4H2,(H2,14,15,16)(H2,20,21,22)/t7-,9-,10-,13-/m1/s1" 5JO InChIKey InChI 1.03 ODQWOSMBGNICLO-QYVSTXNMSA-N 5JO SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3OCC#C" 5JO SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3OCC#C" 5JO SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "C#CCO[C@@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2ncnc3N)COP(=O)(O)O)O" 5JO SMILES "OpenEye OEToolkits" 1.9.2 "C#CCOC1C(C(OC1n2cnc3c2ncnc3N)COP(=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 5JO "SYSTEMATIC NAME" ACDLabs 12.01 "2'-O-prop-2-yn-1-yladenosine 5'-(dihydrogen phosphate)" 5JO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3-oxidanyl-4-prop-2-ynoxy-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 5JO "Create component" 2015-10-02 RCSB 5JO "Modify synonyms" 2015-10-05 RCSB 5JO "Initial release" 2015-12-02 RCSB 5JO "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 5JO _pdbx_chem_comp_synonyms.name "2'-Propargyl-Adenosine" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##