data_9SI # _chem_comp.id 9SI _chem_comp.name "[(2R,3S,4R,5R)-5-[1-[[4-(aminomethyl)phenyl]methyl]-6-azanyl-purin-1-ium-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C18 H24 N6 O7 P" _chem_comp.mon_nstd_parent_comp_id A _chem_comp.pdbx_synonyms 1-benzylamine-adenosine _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2021-11-19 _chem_comp.pdbx_modified_date 2022-08-22 _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 467.393 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 9SI _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 7Q7Z _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # 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 9SI C4 C1 C 0 1 Y N N 34.147 -50.600 3.423 0.660 0.292 -0.975 C4 9SI 1 9SI C5 C2 C 0 1 Y N N 33.627 -50.048 2.162 1.261 1.449 -0.451 C5 9SI 2 9SI C6 C3 C 0 1 Y N N 33.039 -48.688 2.195 2.612 1.689 -0.753 C6 9SI 3 9SI C1 C4 C 0 1 N N N 32.428 -46.685 3.388 4.665 1.043 -1.846 C1 9SI 4 9SI C2 C5 C 0 1 Y N N 33.506 -48.598 4.481 2.648 -0.261 -1.987 C2 9SI 5 9SI C3 C6 C 0 1 Y N N 32.797 -45.934 4.649 5.533 0.504 -0.738 C3 9SI 6 9SI N1 N1 N 1 1 Y N N 33.014 -48.032 3.360 3.255 0.813 -1.518 N1 9SI 7 9SI C7 C7 C 0 1 Y N N 34.017 -45.269 4.731 5.976 -0.805 -0.783 C7 9SI 8 9SI C9 C8 C 0 1 Y N N 34.356 -44.576 5.888 6.772 -1.300 0.233 C9 9SI 9 9SI C10 C9 C 0 1 Y N N 33.474 -44.543 6.961 7.125 -0.486 1.293 C10 9SI 10 9SI C11 C10 C 0 1 Y N N 32.253 -45.203 6.879 6.683 0.822 1.337 C11 9SI 11 9SI C12 C11 C 0 1 Y N N 31.914 -45.895 5.723 5.891 1.319 0.319 C12 9SI 12 9SI C13 C12 C 0 1 N N N 33.842 -43.791 8.219 7.993 -1.026 2.401 C13 9SI 13 9SI C8 C13 C 0 1 Y N N 34.425 -52.044 1.822 -0.799 1.428 0.227 C8 9SI 14 9SI "C1'" C14 C 0 1 N N R 35.237 -52.772 4.068 -1.662 -0.703 -0.813 "C1'" 9SI 15 9SI "C2'" C15 C 0 1 N N R 34.599 -54.155 4.044 -1.603 -1.853 0.226 "C2'" 9SI 16 9SI "C3'" C16 C 0 1 N N S 35.740 -55.032 4.557 -3.045 -2.414 0.170 "C3'" 9SI 17 9SI "C4'" C17 C 0 1 N N R 36.992 -54.324 4.036 -3.876 -1.262 -0.427 "C4'" 9SI 18 9SI "C5'" C18 C 0 1 N N N 37.640 -54.980 2.842 -4.990 -0.866 0.545 "C5'" 9SI 19 9SI N10 N2 N 0 1 N N N 32.785 -43.975 9.228 9.406 -0.796 2.072 N10 9SI 20 9SI N3 N3 N 0 1 Y N N 34.056 -49.828 4.533 1.384 -0.527 -1.731 N3 9SI 21 9SI N6 N4 N 0 1 N N N 32.543 -48.122 1.069 3.257 2.812 -0.266 N6 9SI 22 9SI N7 N5 N 0 1 Y N N 33.828 -50.985 1.219 0.316 2.097 0.272 N7 9SI 23 9SI N9 N6 N 0 1 Y N N 34.619 -51.822 3.136 -0.637 0.303 -0.527 N9 9SI 24 9SI "O2'" O1 O 0 1 N N N 33.425 -54.202 4.827 -0.654 -2.846 -0.166 "O2'" 9SI 25 9SI "O3'" O2 O 0 1 N N N 35.757 -55.030 5.982 -3.102 -3.563 -0.677 "O3'" 9SI 26 9SI "O4'" O3 O 0 1 N N N 36.582 -52.972 3.687 -2.984 -0.153 -0.631 "O4'" 9SI 27 9SI "O5'" O4 O 0 1 N N N 39.038 -54.710 2.784 -5.825 0.121 -0.064 "O5'" 9SI 28 9SI OP1 O5 O 0 1 N N N 39.512 -55.492 0.468 -8.011 -0.310 1.121 OP1 9SI 29 9SI OP2 O6 O 0 1 N N N 41.132 -53.861 1.716 -6.608 1.617 1.951 OP2 9SI 30 9SI P P1 P 0 1 N N N 39.729 -54.325 1.403 -7.100 0.768 0.675 P 9SI 31 9SI H1 H1 H 0 1 N N N 32.794 -46.120 2.518 4.842 2.113 -1.958 H1 9SI 32 9SI H3 H2 H 0 1 N N N 31.333 -46.773 3.334 4.908 0.535 -2.779 H3 9SI 33 9SI H2 H3 H 0 1 N N N 33.456 -48.029 5.397 3.208 -0.947 -2.605 H2 9SI 34 9SI H4 H4 H 0 1 N N N 34.701 -45.291 3.895 5.699 -1.441 -1.611 H4 9SI 35 9SI H5 H5 H 0 1 N N N 35.305 -44.064 5.952 7.117 -2.323 0.199 H5 9SI 36 9SI H6 H6 H 0 1 N N N 31.568 -45.178 7.714 6.959 1.458 2.165 H6 9SI 37 9SI H7 H7 H 0 1 N N N 30.963 -46.403 5.658 5.548 2.343 0.351 H7 9SI 38 9SI H10 H8 H 0 1 N N N 34.795 -44.177 8.611 7.749 -0.518 3.333 H10 9SI 39 9SI H9 H9 H 0 1 N N N 33.947 -42.720 7.989 7.815 -2.096 2.513 H9 9SI 40 9SI H8 H10 H 0 1 N N N 34.709 -52.952 1.311 -1.716 1.717 0.719 H8 9SI 41 9SI "H1'" H11 H 0 1 N N N 35.183 -52.373 5.092 -1.544 -1.093 -1.824 "H1'" 9SI 42 9SI "H2'" H12 H 0 1 N N N 34.379 -54.429 3.002 -1.374 -1.468 1.219 "H2'" 9SI 43 9SI "H3'" H13 H 0 1 N N N 35.667 -56.048 4.142 -3.397 -2.661 1.172 "H3'" 9SI 44 9SI "H4'" H14 H 0 1 N N N 37.728 -54.280 4.852 -4.308 -1.571 -1.379 "H4'" 9SI 45 9SI "H5'" H15 H 0 1 N N N 37.165 -54.599 1.925 -5.586 -1.744 0.792 "H5'" 9SI 46 9SI "H5''" H16 H 0 0 N N N 37.490 -56.068 2.908 -4.549 -0.458 1.455 "H5''" 9SI 47 9SI H17 H17 H 0 1 N N N 33.028 -43.477 10.061 9.583 0.182 1.900 H17 9SI 48 9SI H18 H18 H 0 1 N N N 31.919 -43.624 8.871 10.009 -1.150 2.800 H18 9SI 49 9SI H61 H20 H 0 1 N N N 32.152 -47.202 1.102 2.777 3.444 0.291 H61 9SI 50 9SI H62 H21 H 0 1 N N N 32.568 -48.624 0.204 4.190 2.967 -0.481 H62 9SI 51 9SI "HO2'" H22 H 0 0 N N N 33.054 -55.076 4.790 -0.581 -3.586 0.452 "HO2'" 9SI 52 9SI "HO3'" H23 H 0 0 N Y N 34.981 -55.469 6.309 -2.550 -4.299 -0.379 "HO3'" 9SI 53 9SI HOP2 H25 H 0 0 N N N 41.757 -54.403 1.249 -6.006 2.342 1.733 HOP2 9SI 54 9SI OP3 O7 O 0 1 N Y N 38.862 -53.068 0.901 -7.878 1.738 -0.347 OP3 9SI 55 9SI HOP3 H26 H 0 0 N Y N 38.384 -53.306 0.115 -8.660 2.164 0.031 HOP3 9SI 56 # 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 9SI OP1 P DOUB N N 1 9SI N6 C6 SING N N 2 9SI N7 C8 DOUB Y N 3 9SI N7 C5 SING Y N 4 9SI P OP2 SING N N 5 9SI P "O5'" SING N N 6 9SI C8 N9 SING Y N 7 9SI C5 C6 DOUB Y N 8 9SI C5 C4 SING Y N 9 9SI C6 N1 SING Y N 10 9SI "O5'" "C5'" SING N N 11 9SI "C5'" "C4'" SING N N 12 9SI N9 C4 SING Y N 13 9SI N9 "C1'" SING N N 14 9SI N1 C1 SING N N 15 9SI N1 C2 DOUB Y N 16 9SI C1 C3 SING N N 17 9SI C4 N3 DOUB Y N 18 9SI "O4'" "C4'" SING N N 19 9SI "O4'" "C1'" SING N N 20 9SI "C4'" "C3'" SING N N 21 9SI "C2'" "C1'" SING N N 22 9SI "C2'" "C3'" SING N N 23 9SI "C2'" "O2'" SING N N 24 9SI C2 N3 SING Y N 25 9SI "C3'" "O3'" SING N N 26 9SI C3 C7 DOUB Y N 27 9SI C3 C12 SING Y N 28 9SI C7 C9 SING Y N 29 9SI C12 C11 DOUB Y N 30 9SI C9 C10 DOUB Y N 31 9SI C11 C10 SING Y N 32 9SI C10 C13 SING N N 33 9SI C13 N10 SING N N 34 9SI C1 H1 SING N N 35 9SI C1 H3 SING N N 36 9SI C2 H2 SING N N 37 9SI C7 H4 SING N N 38 9SI C9 H5 SING N N 39 9SI C11 H6 SING N N 40 9SI C12 H7 SING N N 41 9SI C13 H10 SING N N 42 9SI C13 H9 SING N N 43 9SI C8 H8 SING N N 44 9SI "C1'" "H1'" SING N N 45 9SI "C2'" "H2'" SING N N 46 9SI "C3'" "H3'" SING N N 47 9SI "C4'" "H4'" SING N N 48 9SI "C5'" "H5'" SING N N 49 9SI "C5'" "H5''" SING N N 50 9SI N10 H17 SING N N 51 9SI N10 H18 SING N N 52 9SI N6 H61 SING N N 53 9SI N6 H62 SING N N 54 9SI "O2'" "HO2'" SING N N 55 9SI "O3'" "HO3'" SING N N 56 9SI OP2 HOP2 SING N N 57 9SI OP3 P SING N N 58 9SI OP3 HOP3 SING N N 59 # 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 9SI InChI InChI 1.06 "InChI=1S/C18H23N6O7P/c19-5-10-1-3-11(4-2-10)6-23-8-22-17-13(16(23)20)21-9-24(17)18-15(26)14(25)12(31-18)7-30-32(27,28)29/h1-4,8-9,12,14-15,18,20,25-26H,5-7,19H2,(H2,27,28,29)/p+1/t12-,14-,15-,18-/m1/s1" 9SI InChIKey InChI 1.06 BZYUSKWOMPCXQZ-SCFUHWHPSA-O 9SI SMILES_CANONICAL CACTVS 3.385 "NCc1ccc(C[n+]2cnc3n(cnc3c2N)[C@@H]4O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]4O)cc1" 9SI SMILES CACTVS 3.385 "NCc1ccc(C[n+]2cnc3n(cnc3c2N)[CH]4O[CH](CO[P](O)(O)=O)[CH](O)[CH]4O)cc1" 9SI SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(ccc1CN)C[n+]2cnc3c(c2N)ncn3[C@H]4[C@@H]([C@@H]([C@H](O4)COP(=O)(O)O)O)O" 9SI SMILES "OpenEye OEToolkits" 2.0.7 "c1cc(ccc1CN)C[n+]2cnc3c(c2N)ncn3C4C(C(C(O4)COP(=O)(O)O)O)O" # _pdbx_chem_comp_identifier.comp_id 9SI _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "[(2~{R},3~{S},4~{R},5~{R})-5-[1-[[4-(aminomethyl)phenyl]methyl]-6-azanyl-purin-1-ium-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 9SI _pdbx_chem_comp_synonyms.name 1-benzylamine-adenosine _pdbx_chem_comp_synonyms.provenance AUTHOR _pdbx_chem_comp_synonyms.type ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 9SI "Create component" 2021-11-19 PDBE 9SI "Modify aromatic_flag" 2022-03-14 PDBE 9SI "Modify leaving atom flag" 2022-03-15 PDBE 9SI "Initial release" 2022-03-23 RCSB 9SI "Modify descriptor" 2022-08-22 RCSB #