data_SGV # _chem_comp.id SGV _chem_comp.name SANGIVAMYCIN _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAD _chem_comp.formula "C12 H15 N5 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "4-amino-7-beta-D-ribofuranosyl-7H-pyrrolo[2,3-d]pyrimidine-5-carboxamide" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-07-27 _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 309.278 _chem_comp.one_letter_code ? _chem_comp.three_letter_code SGV _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 3NYN _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 SGV N1 N1 N 0 1 Y N N -48.594 54.141 -40.861 3.476 -2.207 -0.433 N1 SGV 1 SGV C2 C2 C 0 1 Y N N -47.388 54.624 -41.215 2.347 -2.860 -0.639 C2 SGV 2 SGV N3 N3 N 0 1 Y N N -47.242 55.584 -42.150 1.170 -2.273 -0.606 N3 SGV 3 SGV C4 C4 C 0 1 Y N N -48.312 56.121 -42.792 1.067 -0.968 -0.357 C4 SGV 4 SGV C5 C5 C 0 1 Y N N -49.657 55.647 -42.459 2.243 -0.234 -0.132 C5 SGV 5 SGV C6 C6 C 0 1 Y N N -49.737 54.594 -41.425 3.474 -0.901 -0.178 C6 SGV 6 SGV N6 N6 N 0 1 N N N -50.930 54.099 -41.055 4.658 -0.218 0.038 N6 SGV 7 SGV C7 C7 C 0 1 Y N N -50.516 56.339 -43.232 1.817 1.153 0.109 C7 SGV 8 SGV C8 C8 C 0 1 Y N N -49.785 57.184 -43.994 0.457 1.157 0.016 C8 SGV 9 SGV N9 N9 N 0 1 Y N N -48.480 57.051 -43.724 0.014 -0.096 -0.260 N9 SGV 10 SGV "C1'" "C1'" C 0 1 N N R -47.398 57.804 -44.373 -1.393 -0.466 -0.430 "C1'" SGV 11 SGV C10 C10 C 0 1 N N N -52.002 56.218 -43.265 2.685 2.305 0.395 C10 SGV 12 SGV N11 N11 N 0 1 N N N -52.725 57.258 -43.678 2.345 3.531 -0.049 N11 SGV 13 SGV O12 O12 O 0 1 N N N -52.530 55.173 -42.917 3.710 2.151 1.032 O12 SGV 14 SGV "C2'" "C2'" C 0 1 N N R -47.086 56.970 -45.604 -1.982 -1.000 0.901 "C2'" SGV 15 SGV "O2'" "O2'" O 0 1 N N N -45.680 56.905 -45.818 -1.734 -2.400 1.043 "O2'" SGV 16 SGV "C3'" "C3'" C 0 1 N N S -47.803 57.694 -46.721 -3.494 -0.722 0.721 "C3'" SGV 17 SGV "O3'" "O3'" O 0 1 N N N -47.128 57.540 -47.975 -4.170 -1.901 0.278 "O3'" SGV 18 SGV "C4'" "C4'" C 0 1 N N R -47.840 59.145 -46.247 -3.551 0.372 -0.362 "C4'" SGV 19 SGV "O4'" "O4'" O 0 1 N N N -47.841 59.089 -44.816 -2.196 0.702 -0.708 "O4'" SGV 20 SGV "C5'" "C5'" C 0 1 N N N -49.019 59.977 -46.752 -4.265 1.610 0.185 "C5'" SGV 21 SGV "O5'" "O5'" O 0 1 N N N -50.235 59.223 -46.792 -4.416 2.573 -0.859 "O5'" SGV 22 SGV H2 H2 H 0 1 N N N -46.506 54.228 -40.733 2.392 -3.919 -0.844 H2 SGV 23 SGV HN6 HN6 H 0 1 N N N -50.798 53.401 -40.351 5.481 -0.710 0.188 HN6 SGV 24 SGV HN6A HN6A H 0 0 N N N -51.498 54.837 -40.691 4.666 0.752 0.038 HN6A SGV 25 SGV H8 H8 H 0 1 N N N -50.196 57.870 -44.719 -0.173 2.026 0.142 H8 SGV 26 SGV "H1'" "H1'" H 0 1 N N N -46.551 57.968 -43.690 -1.502 -1.206 -1.222 "H1'" SGV 27 SGV HN11 HN11 H 0 0 N N N -53.722 57.193 -43.708 1.528 3.654 -0.558 HN11 SGV 28 SGV HN1A HN1A H 0 0 N N N -52.270 58.103 -43.958 2.918 4.291 0.139 HN1A SGV 29 SGV "H2'" "H2'" H 0 1 N N N -47.414 55.923 -45.520 -1.583 -0.448 1.752 "H2'" SGV 30 SGV "HO2'" "HO2'" H 0 0 N N N -45.501 56.381 -46.590 -2.083 -2.780 1.860 "HO2'" SGV 31 SGV "H3'" "H3'" H 0 1 N N N -48.811 57.296 -46.911 -3.929 -0.362 1.654 "H3'" SGV 32 SGV "HO3'" "HO3'" H 0 0 N N N -47.605 58.006 -48.651 -5.121 -1.783 0.149 "HO3'" SGV 33 SGV "H4'" "H4'" H 0 1 N N N -46.966 59.665 -46.666 -4.077 -0.003 -1.240 "H4'" SGV 34 SGV "H5'" "H5'" H 0 1 N N N -49.159 60.833 -46.075 -5.247 1.326 0.563 "H5'" SGV 35 SGV "H5'A" "H5'A" H 0 0 N N N -48.790 60.327 -47.769 -3.675 2.041 0.994 "H5'A" SGV 36 SGV "HO5'" "HO5'" H 0 0 N N N -50.940 59.775 -47.110 -4.861 3.386 -0.583 "HO5'" SGV 37 # # 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 SGV N1 C2 DOUB Y N 1 SGV N1 C6 SING Y N 2 SGV C2 N3 SING Y N 3 SGV N3 C4 DOUB Y N 4 SGV C4 C5 SING Y N 5 SGV C4 N9 SING Y N 6 SGV C5 C6 DOUB Y N 7 SGV C5 C7 SING Y N 8 SGV C6 N6 SING N N 9 SGV C7 C8 DOUB Y N 10 SGV C7 C10 SING N N 11 SGV C8 N9 SING Y N 12 SGV N9 "C1'" SING N N 13 SGV "C1'" "C2'" SING N N 14 SGV "C1'" "O4'" SING N N 15 SGV C10 N11 SING N N 16 SGV C10 O12 DOUB N N 17 SGV "C2'" "O2'" SING N N 18 SGV "C2'" "C3'" SING N N 19 SGV "C3'" "O3'" SING N N 20 SGV "C3'" "C4'" SING N N 21 SGV "C4'" "O4'" SING N N 22 SGV "C4'" "C5'" SING N N 23 SGV "C5'" "O5'" SING N N 24 SGV C2 H2 SING N N 25 SGV N6 HN6 SING N N 26 SGV N6 HN6A SING N N 27 SGV C8 H8 SING N N 28 SGV "C1'" "H1'" SING N N 29 SGV N11 HN11 SING N N 30 SGV N11 HN1A SING N N 31 SGV "C2'" "H2'" SING N N 32 SGV "O2'" "HO2'" SING N N 33 SGV "C3'" "H3'" SING N N 34 SGV "O3'" "HO3'" SING N N 35 SGV "C4'" "H4'" SING N N 36 SGV "C5'" "H5'" SING N N 37 SGV "C5'" "H5'A" SING N N 38 SGV "O5'" "HO5'" SING N N 39 # # 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 SGV SMILES ACDLabs 12.01 "O=C(c2c1c(ncnc1n(c2)C3OC(C(O)C3O)CO)N)N" SGV SMILES_CANONICAL CACTVS 3.370 "NC(=O)c1cn([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c3ncnc(N)c13" SGV SMILES CACTVS 3.370 "NC(=O)c1cn([CH]2O[CH](CO)[CH](O)[CH]2O)c3ncnc(N)c13" SGV SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "c1c(c2c(ncnc2n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N)C(=O)N" SGV SMILES "OpenEye OEToolkits" 1.7.0 "c1c(c2c(ncnc2n1C3C(C(C(O3)CO)O)O)N)C(=O)N" SGV InChI InChI 1.03 "InChI=1S/C12H15N5O5/c13-9-6-4(10(14)21)1-17(11(6)16-3-15-9)12-8(20)7(19)5(2-18)22-12/h1,3,5,7-8,12,18-20H,2H2,(H2,14,21)(H2,13,15,16)/t5-,7-,8-,12-/m1/s1" SGV InChIKey InChI 1.03 OBZJZDHRXBKKTJ-JTFADIMSSA-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 SGV "SYSTEMATIC NAME" ACDLabs 12.01 "4-amino-7-(beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine-5-carboxamide" SGV "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "4-azanyl-7-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrrolo[2,3-d]pyrimidine-5-carboxamide" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site SGV "Create component" 2010-07-27 RCSB SGV "Modify aromatic_flag" 2011-06-04 RCSB SGV "Modify descriptor" 2011-06-04 RCSB SGV "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id SGV _pdbx_chem_comp_synonyms.name "4-amino-7-beta-D-ribofuranosyl-7H-pyrrolo[2,3-d]pyrimidine-5-carboxamide" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##