data_VDA
#
_chem_comp.id VDA
_chem_comp.name "(1R,2R,3R,5Z)-17-{(1S)-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 "(20S)-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 VDA
_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 2ZL9
_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
VDA O2 O2 O 0 1 N N N 16.341 8.598 19.342 6.511 1.467 0.718 O2 VDA 1
VDA C1 C1 C 0 1 N N R 14.808 6.038 19.069 5.293 -1.082 0.352 C1 VDA 2
VDA C2 C2 C 0 1 N N N 14.284 7.441 18.444 6.490 -0.628 -0.485 C2 VDA 3
VDA C3 C3 C 0 1 N N R 14.911 8.713 19.348 6.500 0.897 -0.592 C3 VDA 4
VDA C4 C4 C 0 1 N N N 14.394 8.548 20.899 5.247 1.363 -1.342 C4 VDA 5
VDA C5 C5 C 0 1 N N N 14.551 7.136 21.544 4.031 0.795 -0.645 C5 VDA 6
VDA C6 C6 C 0 1 N N N 14.434 6.930 22.870 3.020 1.581 -0.291 C6 VDA 7
VDA C7 C7 C 0 1 N N N 14.950 5.820 23.721 1.791 0.993 0.266 C7 VDA 8
VDA C8 C8 C 0 1 N N N 14.727 5.701 24.946 0.743 1.768 0.525 C8 VDA 9
VDA C9 C9 C 0 1 N N N 14.513 6.971 26.034 0.742 3.271 0.271 C9 VDA 10
VDA C10 C10 C 0 1 N N N 14.254 5.919 20.542 3.995 -0.690 -0.362 C10 VDA 11
VDA C11 C11 C 0 1 N N N 13.256 6.821 27.019 -0.475 3.687 -0.552 C11 VDA 12
VDA C12 C12 C 0 1 N N N 13.092 5.250 27.577 -1.780 3.086 0.001 C12 VDA 13
VDA C13 C13 C 0 1 N N S 13.302 4.041 26.408 -1.613 1.595 0.024 C13 VDA 14
VDA C14 C14 C 0 1 N N S 14.728 4.352 25.728 -0.544 1.235 1.087 C14 VDA 15
VDA C15 C15 C 0 1 N N N 15.217 2.898 25.026 -0.741 -0.283 1.082 C15 VDA 16
VDA C16 C16 C 0 1 N N N 14.366 1.844 25.787 -2.246 -0.419 0.870 C16 VDA 17
VDA C17 C17 C 0 1 N N N 13.624 2.598 26.944 -2.730 0.665 0.301 C17 VDA 18
VDA C18 C18 C 0 1 N N N 11.938 4.196 25.417 -1.029 1.184 -1.329 C18 VDA 19
VDA C20 C20 C 0 1 N N S 12.798 2.164 28.343 -4.181 0.911 -0.027 C20 VDA 20
VDA C21 C21 C 0 1 N N N 13.549 0.791 28.732 -4.731 2.010 0.885 C21 VDA 21
VDA S22 S22 S 0 1 N N N 11.124 2.228 28.324 -5.126 -0.616 0.228 S22 VDA 22
VDA C23 C23 C 0 1 N N N 10.551 1.217 27.346 -6.785 -0.172 -0.355 C23 VDA 23
VDA C25 C25 C 0 1 N N N 9.335 0.372 27.818 -7.718 -1.375 -0.204 C25 VDA 24
VDA O3 O3 O 0 1 N N N 10.242 -0.752 28.394 -7.875 -1.685 1.182 O3 VDA 25
VDA C26 C26 C 0 1 N N N 8.236 0.757 28.508 -9.083 -1.041 -0.809 C26 VDA 26
VDA C27 C27 C 0 1 N N N 9.195 -0.373 26.391 -7.118 -2.580 -0.931 C27 VDA 27
VDA O1 O1 O 0 1 N N N 14.389 4.919 18.298 5.337 -2.500 0.518 O1 VDA 28
VDA O4 O4 O 0 1 N N N 14.625 7.620 17.080 7.699 -1.069 0.137 O4 VDA 29
VDA C30 C30 C 0 1 N N N 13.538 8.121 16.456 8.764 -1.326 -0.780 C30 VDA 30
VDA C31 C31 C 0 1 N N N 14.128 8.244 14.878 10.001 -1.789 -0.007 C31 VDA 31
VDA O5 O5 O 0 1 N N N 13.768 6.985 14.292 9.729 -3.045 0.619 O5 VDA 32
VDA C29 C29 C 0 1 N N N 7.387 1.974 27.706 -9.650 0.208 -0.131 C29 VDA 33
VDA C28 C28 C 0 1 N N N 8.167 -1.624 26.236 -8.052 -3.783 -0.782 C28 VDA 34
VDA HO2 HO2 H 0 1 N N N 16.653 8.573 18.445 6.517 2.434 0.726 HO2 VDA 35
VDA H1 H1 H 0 1 N N N 15.908 6.035 19.062 5.330 -0.600 1.329 H1 VDA 36
VDA H2 H2 H 0 1 N N N 13.185 7.420 18.491 6.419 -1.061 -1.483 H2 VDA 37
VDA H3 H3 H 0 1 N N N 14.592 9.680 18.933 7.389 1.218 -1.135 H3 VDA 38
VDA H4 H4 H 0 1 N N N 14.978 9.251 21.512 5.199 2.452 -1.333 H4 VDA 39
VDA H4A H4A H 0 1 N N N 13.311 8.738 20.869 5.281 1.003 -2.371 H4A VDA 40
VDA H6 H6 H 0 1 N N N 13.878 7.689 23.401 3.100 2.651 -0.411 H6 VDA 41
VDA H7 H7 H 0 1 N N N 15.559 5.065 23.246 1.741 -0.067 0.463 H7 VDA 42
VDA H9 H9 H 0 1 N N N 15.418 7.032 26.656 0.724 3.795 1.227 H9 VDA 43
VDA H9A H9A H 0 1 N N N 14.325 7.869 25.427 1.649 3.543 -0.268 H9A VDA 44
VDA H10 H10 H 0 1 N N N 13.160 5.827 20.466 3.913 -1.240 -1.299 H10 VDA 45
VDA H10A H10A H 0 0 N N N 14.780 5.056 20.976 3.142 -0.920 0.277 H10A VDA 46
VDA H11 H11 H 0 1 N N N 13.400 7.489 27.881 -0.554 4.774 -0.542 H11 VDA 47
VDA H11A H11A H 0 0 N N N 12.346 7.085 26.460 -0.338 3.353 -1.580 H11A VDA 48
VDA H12 H12 H 0 1 N N N 13.852 5.093 28.357 -1.959 3.454 1.011 H12 VDA 49
VDA H12A H12A H 0 0 N N N 12.056 5.157 27.933 -2.615 3.355 -0.646 H12A VDA 50
VDA H14 H14 H 0 1 N N N 15.550 4.614 26.411 -0.770 1.679 2.056 H14 VDA 51
VDA H15 H15 H 0 1 N N N 15.017 2.880 23.945 -0.191 -0.742 0.261 H15 VDA 52
VDA H15A H15A H 0 0 N N N 16.300 2.721 25.108 -0.444 -0.714 2.038 H15A VDA 53
VDA H16 H16 H 0 1 N N N 14.298 0.790 25.561 -2.833 -1.280 1.154 H16 VDA 54
VDA H18 H18 H 0 1 N N N 11.033 4.230 26.041 -0.061 1.666 -1.469 H18 VDA 55
VDA H18A H18A H 0 0 N N N 12.014 5.124 24.831 -0.903 0.102 -1.357 H18A VDA 56
VDA H18B H18B H 0 0 N N N 11.881 3.335 24.735 -1.706 1.492 -2.126 H18B VDA 57
VDA H20 H20 H 0 1 N N N 12.855 2.909 29.151 -4.270 1.224 -1.067 H20 VDA 58
VDA H21 H21 H 0 1 N N N 13.720 0.196 27.823 -4.642 1.696 1.926 H21 VDA 59
VDA H21A H21A H 0 0 N N N 14.515 1.023 29.205 -4.163 2.927 0.732 H21A VDA 60
VDA H21B H21B H 0 0 N N N 12.925 0.218 29.433 -5.780 2.187 0.648 H21B VDA 61
VDA H23 H23 H 0 1 N N N 10.224 1.780 26.459 -7.167 0.661 0.236 H23 VDA 62
VDA H23A H23A H 0 0 N N N 11.359 0.488 27.183 -6.735 0.120 -1.404 H23A VDA 63
VDA HO3 HO3 H 0 1 N N N 10.427 -1.390 27.715 -8.251 -0.964 1.706 HO3 VDA 64
VDA H26 H26 H 0 1 N N N 7.574 -0.113 28.631 -8.970 -0.855 -1.878 H26 VDA 65
VDA H26A H26A H 0 0 N N N 8.563 1.151 29.482 -9.763 -1.879 -0.656 H26A VDA 66
VDA H27 H27 H 0 1 N N N 8.858 0.392 25.676 -6.997 -2.343 -1.988 H27 VDA 67
VDA H27A H27A H 0 0 N N N 10.185 -0.824 26.230 -6.146 -2.818 -0.499 H27A VDA 68
VDA HO1 HO1 H 0 1 N N N 14.296 5.178 17.389 4.606 -2.858 1.040 HO1 VDA 69
VDA H30 H30 H 0 1 N N N 12.663 7.459 16.531 8.461 -2.105 -1.480 H30 VDA 70
VDA H30A H30A H 0 0 N N N 13.162 9.064 16.879 8.999 -0.415 -1.329 H30A VDA 71
VDA H31 H31 H 0 1 N N N 13.670 9.087 14.339 10.839 -1.900 -0.696 H31 VDA 72
VDA H31A H31A H 0 0 N N N 15.210 8.440 14.840 10.252 -1.050 0.754 H31A VDA 73
VDA HO5 HO5 H 0 1 N N N 13.688 7.085 13.351 10.472 -3.399 1.128 HO5 VDA 74
VDA H29 H29 H 0 1 N N N 7.202 2.809 28.397 -9.677 0.054 0.948 H29 VDA 75
VDA H29A H29A H 0 0 N N N 7.979 2.331 26.850 -9.017 1.065 -0.360 H29A VDA 76
VDA H29B H29B H 0 0 N N N 6.426 1.576 27.348 -10.660 0.393 -0.498 H29B VDA 77
VDA H28 H28 H 0 1 N N N 7.935 -1.779 25.172 -8.246 -3.962 0.276 H28 VDA 78
VDA H28A H28A H 0 0 N N N 8.631 -2.533 26.646 -8.992 -3.578 -1.294 H28A VDA 79
VDA H28B H28B H 0 0 N N N 7.239 -1.406 26.785 -7.583 -4.663 -1.220 H28B VDA 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
VDA O2 C3 SING N N 1
VDA C1 C2 SING N N 2
VDA C1 C10 SING N N 3
VDA C1 O1 SING N N 4
VDA C2 C3 SING N N 5
VDA C2 O4 SING N N 6
VDA C3 C4 SING N N 7
VDA C4 C5 SING N N 8
VDA C5 C6 DOUB N N 9
VDA C5 C10 SING N N 10
VDA C6 C7 SING N N 11
VDA C7 C8 DOUB N N 12
VDA C8 C9 SING N N 13
VDA C8 C14 SING N N 14
VDA C9 C11 SING N N 15
VDA C11 C12 SING N N 16
VDA C12 C13 SING N N 17
VDA C13 C14 SING N N 18
VDA C13 C17 SING N E 19
VDA C13 C18 SING N N 20
VDA C14 C15 SING N N 21
VDA C15 C16 SING N N 22
VDA C16 C17 DOUB N N 23
VDA C17 C20 SING N N 24
VDA C20 C21 SING N N 25
VDA C20 S22 SING N N 26
VDA S22 C23 SING N N 27
VDA C23 C25 SING N N 28
VDA C25 O3 SING N N 29
VDA C25 C26 SING N N 30
VDA C25 C27 SING N N 31
VDA C26 C29 SING N N 32
VDA C27 C28 SING N N 33
VDA O4 C30 SING N N 34
VDA C30 C31 SING N N 35
VDA C31 O5 SING N N 36
VDA O2 HO2 SING N N 37
VDA C1 H1 SING N N 38
VDA C2 H2 SING N N 39
VDA C3 H3 SING N N 40
VDA C4 H4 SING N N 41
VDA C4 H4A SING N N 42
VDA C6 H6 SING N N 43
VDA C7 H7 SING N N 44
VDA C9 H9 SING N N 45
VDA C9 H9A SING N N 46
VDA C10 H10 SING N N 47
VDA C10 H10A SING N N 48
VDA C11 H11 SING N N 49
VDA C11 H11A SING N N 50
VDA C12 H12 SING N N 51
VDA C12 H12A SING N N 52
VDA C14 H14 SING N N 53
VDA C15 H15 SING N N 54
VDA C15 H15A SING N N 55
VDA C16 H16 SING N N 56
VDA C18 H18 SING N N 57
VDA C18 H18A SING N N 58
VDA C18 H18B SING N N 59
VDA C20 H20 SING N N 60
VDA C21 H21 SING N N 61
VDA C21 H21A SING N N 62
VDA C21 H21B SING N N 63
VDA C23 H23 SING N N 64
VDA C23 H23A SING N N 65
VDA O3 HO3 SING N N 66
VDA C26 H26 SING N N 67
VDA C26 H26A SING N N 68
VDA C27 H27 SING N N 69
VDA C27 H27A SING N N 70
VDA O1 HO1 SING N N 71
VDA C30 H30 SING N N 72
VDA C30 H30A SING N N 73
VDA C31 H31 SING N N 74
VDA C31 H31A SING N N 75
VDA O5 HO5 SING N N 76
VDA C29 H29 SING N N 77
VDA C29 H29A SING N N 78
VDA C29 H29B SING N N 79
VDA C28 H28 SING N N 80
VDA C28 H28A SING N N 81
VDA C28 H28B 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
VDA SMILES ACDLabs 10.04 "O(CCO)C3C(O)C/C(=C/C=C1\CCCC2(C(=CCC12)C(SCC(O)(CC)CC)C)C)CC3O"
VDA SMILES_CANONICAL CACTVS 3.341 "CCC(O)(CC)CS[C@@H](C)C1=CC[C@H]2C(/CCC[C@]12C)=C/C=C3/C[C@@H](O)[C@@H](OCCO)[C@H](O)C3"
VDA 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"
VDA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CCC(CC)(CS[C@@H](C)C1=CC[C@@H]2[C@@]1(CCCC2=CC=C3C[C@H](C([C@@H](C3)O)OCCO)O)C)O"
VDA SMILES "OpenEye OEToolkits" 1.5.0 "CCC(CC)(CSC(C)C1=CCC2C1(CCCC2=CC=C3CC(C(C(C3)O)OCCO)O)C)O"
VDA 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+/m0/s1"
VDA InChIKey InChI 1.03 DUIYWCMQVXJTIP-YYDWSLPPSA-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
VDA "SYSTEMATIC NAME" ACDLabs 10.04 "(1R,2S,3R,5Z,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethoxy)-9,10-secoestra-5,7,16-triene-1,3-diol"
VDA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(1R,3R)-5-[2-[(3aS,7aS)-1-[(1S)-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
VDA "Create component" 2008-04-09 PDBJ
VDA "Modify descriptor" 2011-06-04 RCSB
VDA "Modify synonyms" 2021-03-13 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id VDA
_pdbx_chem_comp_synonyms.name "(20S)-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 ?
##