data_VDB
#
_chem_comp.id VDB
_chem_comp.name "(1R,2S,3R,5Z,7E)-17-{(1R)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethoxy)-9,10-secoestra-5,7,16-triene-1,3-diol"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C28 H46 O5 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "(20R)-1alpha,25-dihydroxy-2beta-(2-hydroxyethoxy)-16-ene-22-thia-26,27-dimethyl-19,24-dinorvitamin D3"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2008-04-09
_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 494.727
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VDB
_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 2ZLA
_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
VDB C29 C29 C 0 1 N N N 7.708 -0.703 29.648 10.066 -1.877 0.073 C29 VDB 1
VDB C26 C26 C 0 1 N N N 8.339 0.463 28.866 8.944 -1.166 0.834 C26 VDB 2
VDB C25 C25 C 0 1 N N N 9.388 0.108 27.776 7.626 -1.340 0.078 C25 VDB 3
VDB C27 C27 C 0 1 N N N 8.728 -0.677 26.603 7.794 -0.847 -1.361 C27 VDB 4
VDB C28 C28 C 0 1 N N N 7.597 0.012 25.814 8.156 0.639 -1.352 C28 VDB 5
VDB O3 O3 O 0 1 N N N 10.417 -0.676 28.379 7.260 -2.721 0.069 O3 VDB 6
VDB C23 C23 C 0 1 N N N 9.931 1.470 27.326 6.530 -0.526 0.770 C23 VDB 7
VDB S22 S22 S 0 1 N N N 11.054 2.400 28.436 5.002 -0.620 -0.202 S22 VDB 8
VDB C20 C20 C 0 1 N N R 12.751 1.734 28.102 3.842 0.388 0.762 C20 VDB 9
VDB C21 C21 C 0 1 N N N 13.702 1.898 29.302 3.590 -0.280 2.116 C21 VDB 10
VDB C17 C17 C 0 1 N N N 13.390 2.429 26.839 2.540 0.511 0.013 C17 VDB 11
VDB C16 C16 C 0 1 N N N 14.169 1.796 25.931 2.203 -0.175 -1.071 C16 VDB 12
VDB C15 C15 C 0 1 N N N 14.642 2.781 24.837 0.827 0.259 -1.569 C15 VDB 13
VDB C14 C14 C 0 1 N N S 14.617 4.042 25.705 0.694 1.667 -0.985 C14 VDB 14
VDB C13 C13 C 0 1 N N S 13.250 3.933 26.458 1.421 1.413 0.369 C13 VDB 15
VDB C18 C18 C 0 1 N N N 11.906 4.076 25.632 0.454 0.608 1.239 C18 VDB 16
VDB C12 C12 C 0 1 N N N 13.304 5.002 27.607 1.625 2.731 1.055 C12 VDB 17
VDB C11 C11 C 0 1 N N N 13.539 6.466 27.087 0.236 3.255 1.467 C11 VDB 18
VDB C9 C9 C 0 1 N N N 14.702 6.580 26.065 -0.705 3.383 0.272 C9 VDB 19
VDB C8 C8 C 0 1 N N N 14.626 5.461 25.014 -0.680 2.124 -0.586 C8 VDB 20
VDB C7 C7 C 0 1 N N N 14.518 5.646 23.647 -1.785 1.478 -0.940 C7 VDB 21
VDB C6 C6 C 0 1 N N N 14.459 6.736 22.779 -3.100 1.982 -0.514 C6 VDB 22
VDB C5 C5 C 0 1 N N N 14.323 6.903 21.417 -4.199 1.286 -0.787 C5 VDB 23
VDB C10 C10 C 0 1 N N N 14.186 5.726 20.443 -5.568 1.838 -0.459 C10 VDB 24
VDB C1 C1 C 0 1 N N R 14.760 6.002 19.046 -6.342 0.782 0.337 C1 VDB 25
VDB O1 O1 O 0 1 N N N 14.386 4.900 18.223 -7.681 1.232 0.549 O1 VDB 26
VDB C4 C4 C 0 1 N N N 14.288 8.357 20.884 -4.112 -0.076 -1.439 C4 VDB 27
VDB C3 C3 C 0 1 N N R 14.718 8.509 19.398 -4.935 -1.067 -0.609 C3 VDB 28
VDB O2 O2 O 0 1 N N N 16.142 8.523 19.425 -4.337 -1.222 0.680 O2 VDB 29
VDB C2 C2 C 0 1 N N N 14.195 7.341 18.473 -6.363 -0.531 -0.447 C2 VDB 30
VDB O4 O4 O 0 1 N N N 14.566 7.624 17.089 -7.156 -1.490 0.254 O4 VDB 31
VDB C30 C30 C 0 1 N N N 13.449 8.187 16.359 -7.804 -2.440 -0.594 C30 VDB 32
VDB C31 C31 C 0 1 N N N 13.967 8.152 14.915 -8.621 -3.413 0.259 C31 VDB 33
VDB O5 O5 O 0 1 N N N 13.713 6.899 14.286 -9.678 -2.704 0.909 O5 VDB 34
VDB H29 H29 H 0 1 N N N 7.557 -1.559 28.973 11.005 -1.753 0.611 H29 VDB 35
VDB H29A H29A H 0 0 N N N 8.377 -0.998 30.470 9.832 -2.938 -0.011 H29A VDB 36
VDB H29B H29B H 0 0 N N N 6.738 -0.386 30.060 10.158 -1.446 -0.924 H29B VDB 37
VDB H26 H26 H 0 1 N N N 7.517 0.990 28.360 8.851 -1.598 1.830 H26 VDB 38
VDB H26A H26A H 0 0 N N N 8.893 1.045 29.617 9.178 -0.105 0.917 H26A VDB 39
VDB H27 H27 H 0 1 N N N 9.528 -0.898 25.881 8.589 -1.412 -1.848 H27 VDB 40
VDB H27A H27A H 0 0 N N N 8.247 -1.542 27.082 6.860 -0.991 -1.906 H27A VDB 41
VDB H28 H28 H 0 1 N N N 6.734 0.176 26.476 7.392 1.196 -0.810 H28 VDB 42
VDB H28A H28A H 0 0 N N N 7.954 0.979 25.431 9.121 0.775 -0.864 H28A VDB 43
VDB H28B H28B H 0 0 N N N 7.296 -0.628 24.972 8.212 1.005 -2.378 H28B VDB 44
VDB HO3 HO3 H 0 1 N N N 11.098 -0.850 27.740 7.136 -3.101 0.949 HO3 VDB 45
VDB H23 H23 H 0 1 N N N 10.495 1.287 26.399 6.352 -0.931 1.766 H23 VDB 46
VDB H23A H23A H 0 0 N N N 9.035 2.105 27.260 6.846 0.513 0.851 H23A VDB 47
VDB H20 H20 H 0 1 N N N 12.624 0.658 27.914 4.266 1.380 0.920 H20 VDB 48
VDB H21 H21 H 0 1 N N N 14.741 1.937 28.944 3.166 -1.271 1.959 H21 VDB 49
VDB H21A H21A H 0 0 N N N 13.462 2.830 29.835 4.532 -0.369 2.658 H21A VDB 50
VDB H21B H21B H 0 0 N N N 13.581 1.044 29.984 2.894 0.326 2.696 H21B VDB 51
VDB H16 H16 H 0 1 N N N 14.425 0.747 25.966 2.816 -0.932 -1.537 H16 VDB 52
VDB H15 H15 H 0 1 N N N 15.633 2.545 24.422 0.800 0.287 -2.658 H15 VDB 53
VDB H15A H15A H 0 0 N N N 14.046 2.810 23.913 0.049 -0.397 -1.178 H15A VDB 54
VDB H14 H14 H 0 1 N N N 15.554 4.036 26.281 1.212 2.405 -1.598 H14 VDB 55
VDB H18 H18 H 0 1 N N N 11.052 4.109 26.324 0.912 0.418 2.210 H18 VDB 56
VDB H18A H18A H 0 0 N N N 11.936 5.004 25.042 -0.467 1.174 1.377 H18A VDB 57
VDB H18B H18B H 0 0 N N N 11.797 3.214 24.957 0.229 -0.340 0.751 H18B VDB 58
VDB H12 H12 H 0 1 N N N 12.344 4.978 28.143 2.247 2.596 1.940 H12 VDB 59
VDB H12A H12A H 0 0 N N N 14.156 4.744 28.254 2.099 3.435 0.372 H12A VDB 60
VDB H11 H11 H 0 1 N N N 12.616 6.808 26.596 -0.201 2.568 2.191 H11 VDB 61
VDB H11A H11A H 0 0 N N N 13.808 7.082 27.958 0.351 4.234 1.934 H11A VDB 62
VDB H9 H9 H 0 1 N N N 14.636 7.553 25.556 -1.720 3.555 0.632 H9 VDB 63
VDB H9A H9A H 0 1 N N N 15.655 6.488 26.607 -0.396 4.232 -0.339 H9A VDB 64
VDB H7 H7 H 0 1 N N N 14.466 4.706 23.117 -1.719 0.584 -1.541 H7 VDB 65
VDB H6 H6 H 0 1 N N N 14.539 7.678 23.300 -3.173 2.918 0.021 H6 VDB 66
VDB H10 H10 H 0 1 N N N 14.726 4.868 20.869 -5.464 2.744 0.138 H10 VDB 67
VDB H10A H10A H 0 0 N N N 13.110 5.538 20.316 -6.102 2.065 -1.382 H10A VDB 68
VDB H1 H1 H 0 1 N N N 15.854 6.107 19.084 -5.855 0.624 1.299 H1 VDB 69
VDB HO1 HO1 H 0 1 N N N 14.303 5.191 17.322 -7.744 2.062 1.041 HO1 VDB 70
VDB H4 H4 H 0 1 N N N 13.255 8.724 20.975 -4.513 -0.024 -2.451 H4 VDB 71
VDB H4A H4A H 0 1 N N N 15.011 8.930 21.482 -3.072 -0.401 -1.470 H4A VDB 72
VDB H3 H3 H 0 1 N N N 14.285 9.424 18.968 -4.962 -2.031 -1.115 H3 VDB 73
VDB HO2 HO2 H 0 1 N N N 16.476 8.526 18.536 -3.430 -1.556 0.655 HO2 VDB 74
VDB H2 H2 H 0 1 N N N 13.099 7.253 18.467 -6.793 -0.357 -1.433 H2 VDB 75
VDB H30 H30 H 0 1 N N N 12.531 7.593 16.484 -8.466 -1.919 -1.285 H30 VDB 76
VDB H30A H30A H 0 0 N N N 13.159 9.192 16.700 -7.054 -2.994 -1.158 H30A VDB 77
VDB H31 H31 H 0 1 N N N 13.461 8.942 14.341 -9.043 -4.190 -0.378 H31 VDB 78
VDB H31A H31A H 0 0 N N N 15.056 8.306 14.940 -7.975 -3.869 1.009 H31A VDB 79
VDB HO5 HO5 H 0 1 N N N 13.656 7.022 13.346 -10.238 -3.259 1.468 HO5 VDB 80
# #
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
VDB C29 C26 SING N N 1
VDB C26 C25 SING N N 2
VDB C25 C27 SING N N 3
VDB C25 O3 SING N N 4
VDB C25 C23 SING N N 5
VDB C27 C28 SING N N 6
VDB C23 S22 SING N N 7
VDB S22 C20 SING N N 8
VDB C20 C21 SING N N 9
VDB C20 C17 SING N N 10
VDB C17 C16 DOUB N N 11
VDB C17 C13 SING N N 12
VDB C16 C15 SING N N 13
VDB C15 C14 SING N N 14
VDB C14 C13 SING N N 15
VDB C14 C8 SING N N 16
VDB C13 C18 SING N N 17
VDB C13 C12 SING N N 18
VDB C12 C11 SING N N 19
VDB C11 C9 SING N N 20
VDB C9 C8 SING N N 21
VDB C8 C7 DOUB N N 22
VDB C7 C6 SING N N 23
VDB C6 C5 DOUB N N 24
VDB C5 C10 SING N N 25
VDB C5 C4 SING N N 26
VDB C10 C1 SING N N 27
VDB C1 O1 SING N N 28
VDB C1 C2 SING N N 29
VDB C4 C3 SING N N 30
VDB C3 O2 SING N N 31
VDB C3 C2 SING N N 32
VDB C2 O4 SING N N 33
VDB O4 C30 SING N N 34
VDB C30 C31 SING N N 35
VDB C31 O5 SING N N 36
VDB C29 H29 SING N N 37
VDB C29 H29A SING N N 38
VDB C29 H29B SING N N 39
VDB C26 H26 SING N N 40
VDB C26 H26A SING N N 41
VDB C27 H27 SING N N 42
VDB C27 H27A SING N N 43
VDB C28 H28 SING N N 44
VDB C28 H28A SING N N 45
VDB C28 H28B SING N N 46
VDB O3 HO3 SING N N 47
VDB C23 H23 SING N N 48
VDB C23 H23A SING N N 49
VDB C20 H20 SING N N 50
VDB C21 H21 SING N N 51
VDB C21 H21A SING N E 52
VDB C21 H21B SING N N 53
VDB C16 H16 SING N N 54
VDB C15 H15 SING N N 55
VDB C15 H15A SING N N 56
VDB C14 H14 SING N N 57
VDB C18 H18 SING N N 58
VDB C18 H18A SING N N 59
VDB C18 H18B SING N N 60
VDB C12 H12 SING N N 61
VDB C12 H12A SING N N 62
VDB C11 H11 SING N N 63
VDB C11 H11A SING N N 64
VDB C9 H9 SING N N 65
VDB C9 H9A SING N N 66
VDB C7 H7 SING N N 67
VDB C6 H6 SING N N 68
VDB C10 H10 SING N N 69
VDB C10 H10A SING N N 70
VDB C1 H1 SING N N 71
VDB O1 HO1 SING N N 72
VDB C4 H4 SING N N 73
VDB C4 H4A SING N N 74
VDB C3 H3 SING N N 75
VDB O2 HO2 SING N N 76
VDB C2 H2 SING N N 77
VDB C30 H30 SING N N 78
VDB C30 H30A SING N N 79
VDB C31 H31 SING N N 80
VDB C31 H31A SING N N 81
VDB O5 HO5 SING N N 82
# #
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
VDB SMILES ACDLabs 10.04 "O(CCO)C3C(O)C/C(=C/C=C1\CCCC2(C(=CCC12)C(SCC(O)(CC)CC)C)C)CC3O"
VDB SMILES_CANONICAL CACTVS 3.341 "CCC(O)(CC)CS[C@H](C)C1=CC[C@H]2\C(CCC[C@]12C)=C\C=C3/C[C@@H](O)[C@H](OCCO)[C@H](O)C3"
VDB SMILES CACTVS 3.341 "CCC(O)(CC)CS[CH](C)C1=CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)[CH](OCCO)[CH](O)C3"
VDB SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CCC(CC)(CS[C@H](C)C1=CC[C@@H]\2[C@@]1(CCC/C2=C\C=C3C[C@H](C([C@@H](C3)O)OCCO)O)C)O"
VDB SMILES "OpenEye OEToolkits" 1.5.0 "CCC(CC)(CSC(C)C1=CCC2C1(CCCC2=CC=C3CC(C(C(C3)O)OCCO)O)C)O"
VDB InChI InChI 1.03 "InChI=1S/C28H46O5S/c1-5-28(32,6-2)18-34-19(3)22-11-12-23-21(8-7-13-27(22,23)4)10-9-20-16-24(30)26(25(31)17-20)33-15-14-29/h9-11,19,23-26,29-32H,5-8,12-18H2,1-4H3/b20-9-,21-10+/t19-,23+,24-,25-,26-,27-/m1/s1"
VDB InChIKey InChI 1.03 DUIYWCMQVXJTIP-XXAWZNHHSA-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
VDB "SYSTEMATIC NAME" ACDLabs 10.04 "(1R,2S,3R,5Z,7E)-17-{(1R)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethoxy)-9,10-secoestra-5,7,16-triene-1,3-diol"
VDB "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(1R,3R)-5-[(2E)-2-[(3aS,7aS)-1-[(1R)-1-(2-ethyl-2-hydroxy-butyl)sulfanylethyl]-7a-methyl-3a,5,6,7-tetrahydro-3H-inden-4-ylidene]ethylidene]-2-(2-hydroxyethoxy)cyclohexane-1,3-diol"
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
VDB "Create component" 2008-04-09 PDBJ
VDB "Modify descriptor" 2011-06-04 RCSB
VDB "Modify synonyms" 2021-03-13 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id VDB
_pdbx_chem_comp_synonyms.name "(20R)-1alpha,25-dihydroxy-2beta-(2-hydroxyethoxy)-16-ene-22-thia-26,27-dimethyl-19,24-dinorvitamin D3"
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
##