data_3L1 # _chem_comp.id 3L1 _chem_comp.name "(2S,3R,5S)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H13 N5 O3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "L-2'-deoxyadenosine" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2008-02-18 _chem_comp.pdbx_modified_date 2021-03-01 _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 251.242 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 3L1 _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 2ZI4 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # # 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 3L1 N6 N6 N 0 1 N N N 23.530 -7.609 17.984 4.832 1.298 -0.417 N6 3L1 1 3L1 C6 C6 C 0 1 Y N N 24.790 -7.813 18.149 3.872 0.358 -0.086 C6 3L1 2 3L1 N1 N1 N 0 1 Y N N 25.438 -8.942 17.957 4.221 -0.865 0.297 N1 3L1 3 3L1 C2 C2 C 0 1 Y N N 26.834 -9.218 18.103 3.311 -1.768 0.615 C2 3L1 4 3L1 N3 N3 N 0 1 Y N N 27.617 -8.098 18.494 2.020 -1.516 0.572 N3 3L1 5 3L1 C4 C4 C 0 1 Y N N 26.981 -6.900 18.708 1.576 -0.320 0.200 C4 3L1 6 3L1 C5 C5 C 0 1 Y N N 25.659 -6.705 18.547 2.504 0.678 -0.142 C5 3L1 7 3L1 N7 N7 N 0 1 Y N N 25.385 -5.418 18.857 1.797 1.786 -0.470 N7 3L1 8 3L1 C8 C8 C 0 1 Y N N 26.597 -4.837 19.158 0.525 1.539 -0.349 C8 3L1 9 3L1 N9 N9 N 0 1 Y N N 27.595 -5.791 19.062 0.337 0.250 0.053 N9 3L1 10 3L1 "C1'" "C1'" C 0 1 N N S 29.007 -5.653 19.340 -0.952 -0.401 0.299 "C1'" 3L1 11 3L1 "O4'" "O4'" O 0 1 N N N 29.237 -4.266 19.580 -1.972 0.581 0.581 "O4'" 3L1 12 3L1 "C2'" "C2'" C 0 1 N N N 29.362 -6.297 20.654 -1.466 -1.098 -0.986 "C2'" 3L1 13 3L1 "C3'" "C3'" C 0 1 N N R 30.590 -5.502 21.056 -2.995 -1.139 -0.744 "C3'" 3L1 14 3L1 "O3'" "O3'" O 0 1 N N N 31.792 -6.068 20.554 -3.386 -2.416 -0.235 "O3'" 3L1 15 3L1 "C4'" "C4'" C 0 1 N N S 30.450 -4.159 20.347 -3.240 -0.041 0.309 "C4'" 3L1 16 3L1 "C5'" "C5'" C 0 1 N N N 30.392 -2.997 21.327 -4.221 0.997 -0.240 "C5'" 3L1 17 3L1 "O5'" "O5'" O 0 1 N N N 29.781 -1.809 20.785 -4.519 1.955 0.777 "O5'" 3L1 18 3L1 HN6 HN6 H 0 1 N N N 23.081 -7.556 18.876 5.773 1.067 -0.370 HN6 3L1 19 3L1 HN6A HN6A H 0 0 N N N 23.393 -6.750 17.491 4.565 2.187 -0.699 HN6A 3L1 20 3L1 H2 H2 H 0 1 N N N 27.258 -10.196 17.930 3.639 -2.751 0.921 H2 3L1 21 3L1 H8 H8 H 0 1 N N N 26.745 -3.801 19.426 -0.265 2.248 -0.548 H8 3L1 22 3L1 "H1'" "H1'" H 0 1 N N N 29.575 -6.094 18.508 -0.869 -1.115 1.119 "H1'" 3L1 23 3L1 "H2'" "H2'" H 0 1 N N N 28.551 -6.212 21.392 -1.228 -0.507 -1.870 "H2'" 3L1 24 3L1 "H2'A" "H2'A" H 0 0 N N N 29.535 -7.381 20.587 -1.059 -2.105 -1.072 "H2'A" 3L1 25 3L1 "H3'" "H3'" H 0 1 N N N 30.646 -5.459 22.154 -3.533 -0.915 -1.664 "H3'" 3L1 26 3L1 "HO3'" "HO3'" H 0 0 N N N 31.715 -6.194 19.616 -3.200 -3.152 -0.835 "HO3'" 3L1 27 3L1 "H4'" "H4'" H 0 1 N N N 31.322 -3.948 19.710 -3.638 -0.485 1.222 "H4'" 3L1 28 3L1 "H5'" "H5'" H 0 1 N N N 29.803 -3.316 22.199 -3.774 1.502 -1.096 "H5'" 3L1 29 3L1 "H5'A" "H5'A" H 0 0 N N N 31.430 -2.738 21.583 -5.140 0.499 -0.551 "H5'A" 3L1 30 3L1 "HO5'" "HO5'" H 0 0 N N N 29.647 -1.176 21.481 -5.137 2.645 0.498 "HO5'" 3L1 31 # # 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 3L1 N6 C6 SING N N 1 3L1 C6 N1 DOUB Y N 2 3L1 C6 C5 SING Y N 3 3L1 N1 C2 SING Y N 4 3L1 C2 N3 DOUB Y N 5 3L1 N3 C4 SING Y N 6 3L1 C4 C5 DOUB Y N 7 3L1 C4 N9 SING Y N 8 3L1 C5 N7 SING Y N 9 3L1 N7 C8 DOUB Y N 10 3L1 C8 N9 SING Y N 11 3L1 N9 "C1'" SING N N 12 3L1 "C1'" "O4'" SING N N 13 3L1 "C1'" "C2'" SING N N 14 3L1 "O4'" "C4'" SING N N 15 3L1 "C2'" "C3'" SING N N 16 3L1 "C3'" "O3'" SING N N 17 3L1 "C3'" "C4'" SING N N 18 3L1 "C4'" "C5'" SING N N 19 3L1 "C5'" "O5'" SING N N 20 3L1 N6 HN6 SING N N 21 3L1 N6 HN6A SING N N 22 3L1 C2 H2 SING N N 23 3L1 C8 H8 SING N N 24 3L1 "C1'" "H1'" SING N N 25 3L1 "C2'" "H2'" SING N N 26 3L1 "C2'" "H2'A" SING N N 27 3L1 "C3'" "H3'" SING N N 28 3L1 "O3'" "HO3'" SING N N 29 3L1 "C4'" "H4'" SING N N 30 3L1 "C5'" "H5'" SING N N 31 3L1 "C5'" "H5'A" SING N N 32 3L1 "O5'" "HO5'" SING N N 33 # # 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 3L1 SMILES ACDLabs 10.04 "n2c1c(ncnc1n(c2)C3OC(C(O)C3)CO)N" 3L1 SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2n(cnc12)[C@@H]3C[C@@H](O)[C@H](CO)O3" 3L1 SMILES CACTVS 3.341 "Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO)O3" 3L1 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@@H]3C[C@H]([C@@H](O3)CO)O)N" 3L1 SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3CC(C(O3)CO)O)N" 3L1 InChI InChI 1.03 "InChI=1S/C10H13N5O3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(17)6(2-16)18-7/h3-7,16-17H,1-2H2,(H2,11,12,13)/t5-,6+,7+/m1/s1" 3L1 InChIKey InChI 1.03 OLXZPDWKRNYJJZ-VQVTYTSYSA-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 3L1 "SYSTEMATIC NAME" ACDLabs 10.04 "9-(2-deoxy-beta-L-erythro-pentofuranosyl)-9H-purin-6-amine" 3L1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S,3R,5S)-5-(6-aminopurin-9-yl)-2-(hydroxymethyl)oxolan-3-ol" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 3L1 "Create component" 2008-02-18 PDBJ 3L1 "Modify aromatic_flag" 2011-06-04 RCSB 3L1 "Modify descriptor" 2011-06-04 RCSB 3L1 "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 3L1 _pdbx_chem_comp_synonyms.name "L-2'-deoxyadenosine" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##