data_VSD # _chem_comp.id VSD _chem_comp.name 3-Dehydrosphinganine _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H37 N O2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "(2S,6E)-2-amino-1-hydroxyoctadec-6-en-3-one" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-09-11 _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 299.492 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VSD _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 7K0K _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 VSD C15 C1 C 0 1 N N N 203.072 210.135 214.391 -5.416 -0.292 0.414 C15 VSD 1 VSD C16 C2 C 0 1 N N N 202.374 209.394 215.519 -6.646 0.511 0.078 C16 VSD 2 VSD C10 C3 C 0 1 N N N 207.312 208.112 209.718 0.829 0.449 -0.088 C10 VSD 3 VSD C11 C4 C 0 1 N N N 206.864 208.544 211.152 -0.420 -0.342 0.307 C11 VSD 4 VSD C12 C5 C 0 1 N N N 205.329 208.642 211.414 -1.669 0.474 -0.035 C12 VSD 5 VSD C13 C6 C 0 1 N N N 204.926 209.031 212.869 -2.918 -0.317 0.361 C13 VSD 6 VSD C14 C7 C 0 1 N N N 203.420 209.301 213.125 -4.167 0.499 0.019 C14 VSD 7 VSD C01 C8 C 0 1 N N N 208.820 210.910 198.365 12.069 -0.466 0.039 C01 VSD 8 VSD C02 C9 C 0 1 N N N 208.820 209.975 199.570 10.820 0.349 -0.303 C02 VSD 9 VSD C03 C10 C 0 1 N N N 208.218 210.587 200.843 9.571 -0.441 0.092 C03 VSD 10 VSD C04 C11 C 0 1 N N N 208.629 209.867 202.148 8.322 0.374 -0.249 C04 VSD 11 VSD C05 C12 C 0 1 N N N 207.663 210.066 203.348 7.073 -0.416 0.146 C05 VSD 12 VSD C06 C13 C 0 1 N N N 207.933 209.179 204.594 5.824 0.399 -0.196 C06 VSD 13 VSD C07 C14 C 0 1 N N N 207.341 209.671 205.957 4.575 -0.391 0.199 C07 VSD 14 VSD C08 C15 C 0 1 N N N 207.762 208.836 207.209 3.327 0.424 -0.142 C08 VSD 15 VSD C09 C16 C 0 1 N N N 206.953 209.068 208.527 2.078 -0.366 0.253 C09 VSD 16 VSD C18 C17 C 0 1 N N S 202.353 209.926 216.978 -8.014 -0.048 0.370 C18 VSD 17 VSD C19 C18 C 0 1 N N N 203.193 209.046 217.940 -8.354 -1.128 -0.659 C19 VSD 18 VSD N21 N1 N 0 1 N N N 200.954 209.941 217.449 -9.010 1.029 0.296 N21 VSD 19 VSD O17 O1 O 0 1 N N N 201.806 208.333 215.296 -6.535 1.603 -0.426 O17 VSD 20 VSD O20 O2 O 0 1 N N N 203.623 209.880 218.967 -9.599 -1.739 -0.314 O20 VSD 21 VSD H1 H1 H 0 1 N N N 204.012 210.544 214.791 -5.395 -0.493 1.485 H1 VSD 22 VSD H2 H2 H 0 1 N N N 202.417 210.961 214.078 -5.437 -1.235 -0.132 H2 VSD 23 VSD H3 H3 H 0 1 N N N 206.849 207.137 209.508 0.808 0.650 -1.160 H3 VSD 24 VSD H4 H4 H 0 1 N N N 208.406 208.003 209.734 0.850 1.392 0.458 H4 VSD 25 VSD H5 H5 H 0 1 N N N 207.276 207.813 211.863 -0.441 -1.285 -0.239 H5 VSD 26 VSD H6 H6 H 0 1 N N N 207.299 209.535 211.351 -0.399 -0.542 1.378 H6 VSD 27 VSD H7 H7 H 0 1 N N N 204.915 209.400 210.732 -1.648 1.417 0.511 H7 VSD 28 VSD H8 H8 H 0 1 N N N 205.235 208.209 213.532 -2.939 -1.260 -0.186 H8 VSD 29 VSD H9 H9 H 0 1 N N N 203.023 209.838 212.251 -4.188 0.700 -1.052 H9 VSD 30 VSD H10 H10 H 0 1 N N N 202.916 208.327 213.217 -4.146 1.442 0.565 H10 VSD 31 VSD H11 H11 H 0 1 N N N 209.266 210.395 197.501 12.959 0.097 -0.243 H11 VSD 32 VSD H12 H12 H 0 1 N N N 207.786 211.199 198.126 12.090 -0.667 1.110 H12 VSD 33 VSD H13 H13 H 0 1 N N N 209.408 211.810 198.599 12.048 -1.409 -0.508 H13 VSD 34 VSD H14 H14 H 0 1 N N N 208.239 209.078 199.310 10.841 1.292 0.243 H14 VSD 35 VSD H15 H15 H 0 1 N N N 209.860 209.688 199.784 10.799 0.550 -1.374 H15 VSD 36 VSD H16 H16 H 0 1 N N N 208.545 211.635 200.910 9.550 -1.384 -0.454 H16 VSD 37 VSD H17 H17 H 0 1 N N N 207.122 210.549 200.759 9.592 -0.642 1.163 H17 VSD 38 VSD H18 H18 H 0 1 N N N 208.691 208.789 201.937 8.343 1.317 0.297 H18 VSD 39 VSD H19 H19 H 0 1 N N N 207.730 211.118 203.663 7.052 -1.359 -0.400 H19 VSD 40 VSD H20 H20 H 0 1 N N N 207.513 208.183 204.390 5.846 1.342 0.350 H20 VSD 41 VSD H21 H21 H 0 1 N N N 207.669 210.709 206.115 4.554 -1.334 -0.347 H21 VSD 42 VSD H22 H22 H 0 1 N N N 207.667 207.772 206.945 3.348 1.367 0.404 H22 VSD 43 VSD H23 H23 H 0 1 N N N 207.132 210.102 208.857 2.099 -0.567 1.324 H23 VSD 44 VSD H24 H24 H 0 1 N N N 202.759 210.948 216.987 -8.023 -0.483 1.370 H24 VSD 45 VSD H25 H25 H 0 1 N N N 202.576 208.231 218.346 -8.433 -0.676 -1.648 H25 VSD 46 VSD H26 H26 H 0 1 N N N 204.057 208.621 217.409 -7.568 -1.883 -0.666 H26 VSD 47 VSD H27 H27 H 0 1 N N N 200.922 210.282 218.389 -8.845 1.724 1.009 H27 VSD 48 VSD H28 H28 H 0 1 N N N 200.410 210.538 216.859 -9.021 1.449 -0.622 H28 VSD 49 VSD H30 H30 H 0 1 N N N 204.145 209.380 219.584 -9.878 -2.435 -0.925 H30 VSD 50 VSD H29 H29 H 0 1 N N N 209.620 210.240 202.444 8.301 0.575 -1.321 H29 VSD 51 VSD H31 H31 H 0 1 N N N 206.642 209.852 202.998 7.094 -0.617 1.217 H31 VSD 52 VSD H32 H32 H 0 1 N N N 209.023 209.099 204.715 5.803 0.600 -1.267 H32 VSD 53 VSD H33 H33 H 0 1 N N N 206.244 209.641 205.882 4.596 -0.592 1.271 H33 VSD 54 VSD H34 H34 H 0 1 N N N 208.816 209.068 207.422 3.306 0.625 -1.213 H34 VSD 55 VSD H35 H35 H 0 1 N N N 205.885 208.936 208.297 2.056 -1.309 -0.293 H35 VSD 56 VSD H36 H36 H 0 1 N N N 204.882 207.663 211.188 -1.690 0.675 -1.106 H36 VSD 57 VSD H37 H37 H 0 1 N N N 205.479 209.944 213.135 -2.897 -0.517 1.432 H37 VSD 58 # # 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 VSD C01 C02 SING N N 1 VSD C02 C03 SING N N 2 VSD C03 C04 SING N N 3 VSD C04 C05 SING N N 4 VSD C05 C06 SING N N 5 VSD C06 C07 SING N N 6 VSD C07 C08 SING N N 7 VSD C08 C09 SING N N 8 VSD C09 C10 SING N N 9 VSD C10 C11 SING N N 10 VSD C11 C12 SING N N 11 VSD C12 C13 SING N N 12 VSD C13 C14 SING N N 13 VSD C14 C15 SING N N 14 VSD C15 C16 SING N N 15 VSD O17 C16 DOUB N N 16 VSD C16 C18 SING N N 17 VSD C18 N21 SING N N 18 VSD C18 C19 SING N N 19 VSD C19 O20 SING N N 20 VSD C15 H1 SING N N 21 VSD C15 H2 SING N N 22 VSD C10 H3 SING N N 23 VSD C10 H4 SING N N 24 VSD C11 H5 SING N N 25 VSD C11 H6 SING N N 26 VSD C12 H7 SING N N 27 VSD C13 H8 SING N N 28 VSD C14 H9 SING N N 29 VSD C14 H10 SING N N 30 VSD C01 H11 SING N N 31 VSD C01 H12 SING N N 32 VSD C01 H13 SING N N 33 VSD C02 H14 SING N N 34 VSD C02 H15 SING N N 35 VSD C03 H16 SING N N 36 VSD C03 H17 SING N N 37 VSD C04 H18 SING N N 38 VSD C05 H19 SING N N 39 VSD C06 H20 SING N N 40 VSD C07 H21 SING N N 41 VSD C08 H22 SING N N 42 VSD C09 H23 SING N N 43 VSD C18 H24 SING N N 44 VSD C19 H25 SING N N 45 VSD C19 H26 SING N N 46 VSD N21 H27 SING N N 47 VSD N21 H28 SING N N 48 VSD O20 H30 SING N N 49 VSD C04 H29 SING N N 50 VSD C05 H31 SING N N 51 VSD C06 H32 SING N N 52 VSD C07 H33 SING N N 53 VSD C08 H34 SING N N 54 VSD C09 H35 SING N N 55 VSD C12 H36 SING N N 56 VSD C13 H37 SING N N 57 # # 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 VSD SMILES ACDLabs 12.01 "C(C(C(N)CO)=O)CCCCCCCCCCCCCC" VSD InChI InChI 1.03 "InChI=1S/C18H37NO2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-18(21)17(19)16-20/h17,20H,2-16,19H2,1H3/t17-/m0/s1" VSD InChIKey InChI 1.03 KBUNOSOGGAARKZ-KRWDZBQOSA-N VSD SMILES_CANONICAL CACTVS 3.385 "CCCCCCCCCCCCCCCC(=O)[C@@H](N)CO" VSD SMILES CACTVS 3.385 "CCCCCCCCCCCCCCCC(=O)[CH](N)CO" VSD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCCCCCCCCCCCCCCC(=O)[C@H](CO)N" VSD SMILES "OpenEye OEToolkits" 2.0.7 "CCCCCCCCCCCCCCCC(=O)C(CO)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 VSD "SYSTEMATIC NAME" ACDLabs 12.01 "(2S)-2-amino-1-hydroxyoctadecan-3-one" VSD "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S})-2-azanyl-1-oxidanyl-octadecan-3-one" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site VSD "Create component" 2020-09-11 RCSB VSD "Initial release" 2021-02-24 RCSB VSD "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id VSD _pdbx_chem_comp_synonyms.name "(2S,6E)-2-amino-1-hydroxyoctadec-6-en-3-one" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##