data_NGF # _chem_comp.id NGF _chem_comp.name "3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-D-galacto-non-2-ulosonic acid" _chem_comp.type D-SACCHARIDE _chem_comp.pdbx_type ATOMS _chem_comp.formula "C11 H19 N O10" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "N-glycolylneuraminic acid, ketone form" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-01-04 _chem_comp.pdbx_modified_date 2021-03-13 _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 325.269 _chem_comp.one_letter_code ? _chem_comp.three_letter_code NGF _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 4IMG _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 NGF O10 O10 O 0 1 N N N 28.943 30.744 21.256 -0.036 2.380 -1.056 O10 NGF 1 NGF C10 C10 C 0 1 N N N 28.375 29.703 20.921 -0.044 2.236 0.148 C10 NGF 2 NGF C11 C11 C 0 1 N N N 27.705 29.654 19.551 -0.199 3.434 1.049 C11 NGF 3 NGF N5 N5 N 0 1 N N N 28.397 28.604 21.692 0.082 1.004 0.681 N5 NGF 4 NGF C5 C5 C 0 1 N N R 28.006 27.255 21.185 0.117 -0.171 -0.193 C5 NGF 5 NGF C4 C4 C 0 1 N N S 27.137 26.377 22.094 -1.117 -1.038 0.068 C4 NGF 6 NGF O4 O4 O 0 1 N N N 27.610 26.466 23.466 -1.109 -1.481 1.427 O4 NGF 7 NGF C3 C3 C 0 1 N N N 25.613 26.419 21.713 -2.381 -0.217 -0.193 C3 NGF 8 NGF C6 C6 C 0 1 N N R 29.116 26.304 20.748 1.381 -0.983 0.096 C6 NGF 9 NGF O6 O6 O 0 1 N N N 28.414 25.083 20.349 1.416 -2.130 -0.756 O6 NGF 10 NGF C2 C2 C 0 1 N N N 24.932 27.326 22.671 -3.592 -1.103 -0.056 C2 NGF 11 NGF O2 O2 O 0 1 N N N 25.529 27.545 23.607 -3.458 -2.270 0.222 O2 NGF 12 NGF C1 C1 C 0 1 N N N 23.665 27.961 22.558 -4.956 -0.538 -0.264 C1 NGF 13 NGF O1 O1 O 0 1 N N N 22.843 27.716 21.676 -5.091 0.635 -0.543 O1 NGF 14 NGF O3 O3 O 0 1 N N N 23.394 28.762 23.457 -6.038 -1.329 -0.141 O3 NGF 15 NGF C7 C7 C 0 1 N N S 29.839 26.864 19.534 2.615 -0.117 -0.164 C7 NGF 16 NGF O7 O7 O 0 1 N N N 28.812 27.258 18.592 2.561 0.400 -1.496 O7 NGF 17 NGF C8 C8 C 0 1 N N R 30.813 25.880 18.874 3.878 -0.964 0.004 C8 NGF 18 NGF O8 O8 O 0 1 N N N 31.590 25.213 19.889 3.931 -1.480 1.335 O8 NGF 19 NGF C9 C9 C 0 1 N N N 31.729 26.577 17.870 5.111 -0.097 -0.257 C9 NGF 20 NGF O9 O9 O 0 1 N N N 32.316 27.676 18.559 6.284 -0.913 -0.215 O9 NGF 21 NGF O5 O5 O 0 1 N N N 26.262 29.520 19.551 -0.319 4.616 0.254 O5 NGF 22 NGF H1 H1 H 0 1 N N N 28.122 28.796 19.003 -1.094 3.316 1.661 H1 NGF 23 NGF H2 H2 H 0 1 N N N 27.956 30.584 19.021 0.674 3.519 1.696 H2 NGF 24 NGF H3 H3 H 0 1 N N N 28.687 28.693 22.645 0.148 0.896 1.643 H3 NGF 25 NGF H4 H4 H 0 1 N N N 27.400 27.435 20.285 0.122 0.150 -1.234 H4 NGF 26 NGF H5 H5 H 0 1 N N N 27.426 25.359 21.792 -1.101 -1.902 -0.596 H5 NGF 27 NGF H6 H6 H 0 1 N N N 26.963 26.917 23.996 -1.048 -0.765 2.074 H6 NGF 28 NGF H7 H7 H 0 1 N N N 25.494 26.799 20.688 -2.442 0.597 0.530 H7 NGF 29 NGF H8 H8 H 0 1 N N N 25.182 25.409 21.782 -2.345 0.195 -1.202 H8 NGF 30 NGF H9 H9 H 0 1 N N N 29.820 26.119 21.573 1.376 -1.305 1.138 H9 NGF 31 NGF H10 H10 H 0 1 N N N 27.957 24.721 21.099 1.422 -1.919 -1.699 H10 NGF 32 NGF H11 H11 H 0 1 N N N 22.516 29.101 23.326 -6.901 -0.918 -0.285 H11 NGF 33 NGF H12 H12 H 0 1 N N N 30.407 27.753 19.847 2.635 0.710 0.545 H12 NGF 34 NGF H13 H13 H 0 1 N N N 28.215 27.867 19.010 2.541 -0.282 -2.181 H13 NGF 35 NGF H14 H14 H 0 1 N N N 30.219 25.132 18.328 3.858 -1.791 -0.706 H14 NGF 36 NGF H15 H15 H 0 1 N N N 31.007 24.785 20.505 3.951 -0.799 2.021 H15 NGF 37 NGF H16 H16 H 0 1 N N N 31.147 26.935 17.008 5.028 0.368 -1.240 H16 NGF 38 NGF H17 H17 H 0 1 N N N 32.510 25.885 17.523 5.180 0.677 0.507 H17 NGF 39 NGF H18 H18 H 0 1 N N N 32.898 28.144 17.972 7.106 -0.429 -0.372 H18 NGF 40 NGF H19 H19 H 0 1 N N N 25.945 29.499 18.656 -0.423 5.427 0.769 H19 NGF 41 # # 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 NGF C9 O9 SING N N 1 NGF C9 C8 SING N N 2 NGF O7 C7 SING N N 3 NGF C8 C7 SING N N 4 NGF C8 O8 SING N N 5 NGF C7 C6 SING N N 6 NGF O5 C11 SING N N 7 NGF C11 C10 SING N N 8 NGF O6 C6 SING N N 9 NGF C6 C5 SING N N 10 NGF C10 O10 DOUB N N 11 NGF C10 N5 SING N N 12 NGF C5 N5 SING N N 13 NGF C5 C4 SING N N 14 NGF O1 C1 DOUB N N 15 NGF C3 C4 SING N N 16 NGF C3 C2 SING N N 17 NGF C4 O4 SING N N 18 NGF C1 C2 SING N N 19 NGF C1 O3 SING N N 20 NGF C2 O2 DOUB N N 21 NGF C11 H1 SING N N 22 NGF C11 H2 SING N N 23 NGF N5 H3 SING N N 24 NGF C5 H4 SING N N 25 NGF C4 H5 SING N N 26 NGF O4 H6 SING N N 27 NGF C3 H7 SING N N 28 NGF C3 H8 SING N N 29 NGF C6 H9 SING N N 30 NGF O6 H10 SING N N 31 NGF O3 H11 SING N N 32 NGF C7 H12 SING N N 33 NGF O7 H13 SING N N 34 NGF C8 H14 SING N N 35 NGF O8 H15 SING N N 36 NGF C9 H16 SING N N 37 NGF C9 H17 SING N N 38 NGF O9 H18 SING N N 39 NGF O5 H19 SING N N 40 # # 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 NGF SMILES ACDLabs 12.01 "O=C(O)C(=O)CC(O)C(NC(=O)CO)C(O)C(O)C(O)CO" NGF InChI InChI 1.03 "InChI=1S/C11H19NO10/c13-2-6(17)9(19)10(20)8(12-7(18)3-14)4(15)1-5(16)11(21)22/h4,6,8-10,13-15,17,19-20H,1-3H2,(H,12,18)(H,21,22)/t4-,6+,8+,9+,10+/m0/s1" NGF InChIKey InChI 1.03 SUHQNCLNRUAGOO-KQCZLNONSA-N NGF SMILES_CANONICAL CACTVS 3.370 "OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](NC(=O)CO)[C@@H](O)CC(=O)C(O)=O" NGF SMILES CACTVS 3.370 "OC[CH](O)[CH](O)[CH](O)[CH](NC(=O)CO)[CH](O)CC(=O)C(O)=O" NGF SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C([C@@H]([C@H]([C@H]([C@@H]([C@@H](CO)O)O)O)NC(=O)CO)O)C(=O)C(=O)O" NGF SMILES "OpenEye OEToolkits" 1.7.6 "C(C(C(C(C(C(CO)O)O)O)NC(=O)CO)O)C(=O)C(=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 NGF "SYSTEMATIC NAME" ACDLabs 12.01 "3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-D-galacto-non-2-ulosonic acid" NGF "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(4S,5R,6R,7S,8R)-4,6,7,8,9-pentakis(oxidanyl)-5-(2-oxidanylethanoylamino)-2-oxidanylidene-nonanoic acid" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site NGF "Create component" 2013-01-04 RCSB NGF "Initial release" 2013-11-06 RCSB NGF "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id NGF _pdbx_chem_comp_synonyms.name "N-glycolylneuraminic acid, ketone form" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##