data_VDM # _chem_comp.id VDM _chem_comp.name "(1S,2S,3R,6S)-4-(HYDROXYMETHYL)-6-{[(1S,2S,3S,4R,5R)-2,3,4-TRIHYDROXY-5-(HYDROXYMETHYL)CYCLOHEXYL]AMINO}CYCLOHEX-4-ENE-1,2,3-TRIOL" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C14 H25 N O8" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms VALIDOXYLAMINE _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2007-01-25 _chem_comp.pdbx_modified_date 2021-03-01 _chem_comp.pdbx_ambiguous_flag ? _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 335.350 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VDM _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details "OpenEye/OEToolkits V1.4.2" _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 2JF4 _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 VDM O7 O7 O 0 1 N N N 29.348 51.117 15.007 6.214 2.855 -2.249 O7 VDM 1 VDM C7 C7 C 0 1 N N N 30.453 51.070 14.108 5.686 1.726 -1.579 C7 VDM 2 VDM C5 C5 C 0 1 N N N 30.173 52.166 13.119 4.709 1.019 -2.477 C5 VDM 3 VDM C6 C6 C 0 1 N N N 29.647 51.840 11.917 3.422 0.870 -2.115 C6 VDM 4 VDM C4 C4 C 0 1 N N S 30.406 53.598 13.560 5.233 0.518 -3.805 C4 VDM 5 VDM O4 O4 O 0 1 N N N 31.681 53.801 14.150 6.403 -0.279 -3.608 O4 VDM 6 VDM C3 C3 C 0 1 N N R 30.282 54.586 12.422 4.236 -0.345 -4.599 C3 VDM 7 VDM O3 O3 O 0 1 N N N 30.203 55.886 13.020 4.595 -0.293 -5.983 O3 VDM 8 VDM C2 C2 C 0 1 N N S 29.053 54.227 11.579 2.809 0.181 -4.455 C2 VDM 9 VDM O2 O2 O 0 1 N N N 28.716 55.302 10.696 1.921 -0.644 -5.210 O2 VDM 10 VDM C1 C1 C 0 1 N N S 29.327 52.889 10.854 2.371 0.231 -2.979 C1 VDM 11 VDM "N1'" N1* N 0 1 N N N 30.438 52.957 9.893 2.062 -1.106 -2.458 "N1'" VDM 12 VDM "C1'" C1* C 0 1 N N S 31.198 51.748 9.526 1.557 -1.019 -1.083 "C1'" VDM 13 VDM "C2'" C2* C 0 1 N N S 32.695 51.999 9.340 1.288 -2.416 -0.504 "C2'" VDM 14 VDM "O2'" O2* O 0 1 N N N 33.203 52.878 10.348 2.463 -3.221 -0.597 "O2'" VDM 15 VDM "C6'" C6* C 0 1 N N N 30.573 50.945 8.363 0.274 -0.181 -1.048 "C6'" VDM 16 VDM "C5'" C5* C 0 1 N N R 31.063 51.304 6.955 -0.897 -0.864 -1.772 "C5'" VDM 17 VDM "C7'" C7* C 0 1 N N N 30.546 50.300 5.924 -2.159 -0.002 -1.662 "C7'" VDM 18 VDM "O7'" O7* O 0 1 N N N 29.105 50.280 5.932 -3.206 -0.659 -2.348 "O7'" VDM 19 VDM "C4'" C4* C 0 1 N N R 32.591 51.464 6.910 -1.143 -2.281 -1.223 "C4'" VDM 20 VDM "O4'" O4* O 0 1 N N N 33.027 51.816 5.589 -2.116 -2.921 -2.050 "O4'" VDM 21 VDM "C3'" C3* C 0 1 N N S 33.017 52.518 7.934 0.131 -3.135 -1.203 "C3'" VDM 22 VDM "O3'" O3* O 0 1 N N N 34.416 52.777 7.798 -0.132 -4.339 -0.474 "O3'" VDM 23 VDM H7 H7 H 0 1 N N N 29.525 50.424 15.632 6.808 2.524 -2.945 H7 VDM 24 VDM H7C1 1H7C H 0 0 N N N 30.623 50.070 13.645 6.497 1.053 -1.310 H7C1 VDM 25 VDM H7C2 2H7C H 0 0 N N N 31.449 51.146 14.604 5.173 2.056 -0.679 H7C2 VDM 26 VDM H6 H6 H 0 1 N N N 29.484 50.755 11.807 3.099 1.240 -1.144 H6 VDM 27 VDM H4 H4 H 0 1 N N N 29.607 53.776 14.317 5.542 1.381 -4.407 H4 VDM 28 VDM H1 H1 H 0 1 N N N 28.417 52.629 10.264 1.449 0.821 -2.918 H1 VDM 29 VDM HA HA H 0 1 N N N 31.827 54.698 14.426 6.122 -1.060 -3.108 HA VDM 30 VDM H3 H3 H 0 1 N N N 31.153 54.564 11.726 4.298 -1.401 -4.310 H3 VDM 31 VDM HB HB H 0 1 N N N 30.125 56.507 12.305 4.603 -1.210 -6.299 HB VDM 32 VDM H2 H2 H 0 1 N N N 28.156 54.082 12.225 2.741 1.183 -4.897 H2 VDM 33 VDM HC HC H 0 1 N N N 28.548 56.124 11.141 1.924 -0.293 -6.113 HC VDM 34 VDM "H1'" H1* H 0 1 N N N 31.100 53.660 10.223 1.351 -1.544 -3.038 "H1'" VDM 35 VDM HD HD H 0 1 N N N 31.114 51.085 10.418 2.335 -0.528 -0.489 HD VDM 36 VDM "H2'" H2* H 0 1 N N N 33.210 51.017 9.453 1.067 -2.327 0.568 "H2'" VDM 37 VDM "H6'1" 1H6* H 0 0 N N N 29.461 51.020 8.407 0.459 0.805 -1.494 "H6'1" VDM 38 VDM "H6'2" 2H6* H 0 0 N N N 30.708 49.853 8.543 -0.002 0.001 -0.001 "H6'2" VDM 39 VDM HE HE H 0 1 N N N 34.133 53.034 10.232 2.194 -4.125 -0.377 HE VDM 40 VDM "H3'" H3* H 0 1 N N N 32.465 53.471 7.762 0.410 -3.451 -2.215 "H3'" VDM 41 VDM "H5'" H5* H 0 1 N N N 30.638 52.298 6.684 -0.670 -0.938 -2.844 "H5'" VDM 42 VDM "H7'1" 1H7* H 0 0 N N N 30.978 49.284 6.078 -1.977 0.969 -2.117 "H7'1" VDM 43 VDM "H7'2" 2H7* H 0 0 N N N 30.955 50.499 4.906 -2.428 0.120 -0.616 "H7'2" VDM 44 VDM "H4'" H4* H 0 1 N N N 33.073 50.493 7.170 -1.572 -2.230 -0.215 "H4'" VDM 45 VDM "H7'" H7* H 0 1 N N N 28.784 49.656 5.292 -2.807 -1.124 -3.104 "H7'" VDM 46 VDM HF HF H 0 1 N N N 32.763 51.162 4.953 -1.684 -3.086 -2.901 HF VDM 47 VDM HG HG H 0 1 N N N 34.616 53.099 6.927 0.123 -4.160 0.443 HG VDM 48 # # 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 VDM O7 C7 SING N N 1 VDM O7 H7 SING N N 2 VDM C7 C5 SING N N 3 VDM C7 H7C1 SING N N 4 VDM C7 H7C2 SING N N 5 VDM C5 C6 DOUB N N 6 VDM C5 C4 SING N N 7 VDM C6 C1 SING N N 8 VDM C6 H6 SING N N 9 VDM C4 O4 SING N N 10 VDM C4 C3 SING N N 11 VDM C4 H4 SING N N 12 VDM O4 HA SING N N 13 VDM C3 O3 SING N N 14 VDM C3 C2 SING N N 15 VDM C3 H3 SING N N 16 VDM O3 HB SING N N 17 VDM C2 O2 SING N N 18 VDM C2 C1 SING N N 19 VDM C2 H2 SING N N 20 VDM O2 HC SING N N 21 VDM C1 "N1'" SING N N 22 VDM C1 H1 SING N N 23 VDM "N1'" "C1'" SING N N 24 VDM "N1'" "H1'" SING N N 25 VDM "C1'" HD SING N N 26 VDM "C1'" "C2'" SING N N 27 VDM "C1'" "C6'" SING N N 28 VDM "C2'" "H2'" SING N N 29 VDM "C2'" "O2'" SING N N 30 VDM "C2'" "C3'" SING N N 31 VDM "O2'" HE SING N N 32 VDM "C6'" "H6'1" SING N N 33 VDM "C6'" "H6'2" SING N N 34 VDM "C6'" "C5'" SING N N 35 VDM "C5'" "H5'" SING N N 36 VDM "C5'" "C7'" SING N N 37 VDM "C5'" "C4'" SING N N 38 VDM "C7'" "H7'1" SING N N 39 VDM "C7'" "H7'2" SING N N 40 VDM "C7'" "O7'" SING N N 41 VDM "O7'" "H7'" SING N N 42 VDM "C4'" "H4'" SING N N 43 VDM "C4'" "O4'" SING N N 44 VDM "C4'" "C3'" SING N N 45 VDM "O4'" HF SING N N 46 VDM "C3'" "H3'" SING N N 47 VDM "C3'" "O3'" SING N N 48 VDM "O3'" HG SING N N 49 # # 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 VDM SMILES ACDLabs 10.04 "OC2C(NC1C=C(CO)C(O)C(O)C1O)CC(C(O)C2O)CO" VDM SMILES_CANONICAL CACTVS 3.341 "OC[C@H]1C[C@H](N[C@H]2C=C(CO)[C@@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@@H](O)[C@@H]1O" VDM SMILES CACTVS 3.341 "OC[CH]1C[CH](N[CH]2C=C(CO)[CH](O)[CH](O)[CH]2O)[CH](O)[CH](O)[CH]1O" VDM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H]([C@@H]([C@H]([C@H]1N[C@H]2C=C([C@H]([C@@H]([C@H]2O)O)O)CO)O)O)O)CO" VDM SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(C(C(C1NC2C=C(C(C(C2O)O)O)CO)O)O)O)CO" VDM InChI InChI 1.03 "InChI=1S/C14H25NO8/c16-3-5-1-7(11(20)13(22)9(5)18)15-8-2-6(4-17)10(19)14(23)12(8)21/h1,6-23H,2-4H2/t6-,7+,8+,9-,10-,11+,12+,13+,14+/m1/s1" VDM InChIKey InChI 1.03 YCJYNBLLJHFIIW-MBABXGOBSA-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 VDM "SYSTEMATIC NAME" ACDLabs 10.04 "(1S,2S,3R,6S)-4-(hydroxymethyl)-6-{[(1S,2S,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}cyclohex-4-ene-1,2,3-triol" VDM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(1S,2S,3R,6S)-4-(hydroxymethyl)-6-[[(1S,2S,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino]cyclohex-4-ene-1,2,3-triol" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site VDM "Create component" 2007-01-25 PDBJ VDM "Modify descriptor" 2011-06-04 RCSB VDM "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id VDM _pdbx_chem_comp_synonyms.name VALIDOXYLAMINE _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##