data_VDX
#
_chem_comp.id VDX
_chem_comp.name "5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C27 H44 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "1,25 DIHYDROXY VITAMIN D3"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-11-03
_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 416.636
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VDX
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1DB1
_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
VDX O2 O2 O 0 1 N N N 17.029 18.071 34.819 -1.260 1.799 -7.708 O2 VDX 1
VDX O3 O3 O 0 1 N N N 4.489 26.946 35.054 -2.818 0.819 6.766 O3 VDX 2
VDX C1 C1 C 0 1 N N S 14.139 17.953 35.755 -2.455 -0.546 -5.027 C1 VDX 3
VDX C2 C2 C 0 1 N N N 14.879 16.893 34.895 -2.317 0.041 -6.435 C2 VDX 4
VDX C3 C3 C 0 1 N N R 15.992 17.534 33.962 -1.276 1.161 -6.429 C3 VDX 5
VDX C4 C4 C 0 1 N N N 15.368 18.672 33.049 0.109 0.580 -6.132 C4 VDX 6
VDX C5 C5 C 0 1 N N N 14.622 19.724 33.864 0.050 -0.138 -4.799 C5 VDX 7
VDX C6 C6 C 0 1 N N N 14.797 21.120 33.792 0.998 0.042 -3.856 C6 VDX 8
VDX C7 C7 C 0 1 N N N 14.174 22.286 34.514 0.906 -0.670 -2.580 C7 VDX 9
VDX C8 C8 C 0 1 N N N 13.966 23.488 34.042 1.842 -0.492 -1.648 C8 VDX 10
VDX C9 C9 C 0 1 N N N 14.354 23.927 32.544 3.030 0.437 -1.853 C9 VDX 11
VDX C10 C10 C 0 1 N N N 13.602 19.075 34.828 -1.092 -1.050 -4.585 C10 VDX 12
VDX C11 C11 C 0 1 N N N 13.088 24.490 31.671 3.181 1.389 -0.668 C11 VDX 13
VDX C12 C12 C 0 1 N N N 12.147 25.443 32.564 3.123 0.642 0.674 C12 VDX 14
VDX C13 C13 C 0 1 N N R 11.753 24.897 34.070 1.801 -0.074 0.756 C13 VDX 15
VDX C14 C14 C 0 1 N N S 13.148 24.538 34.777 1.801 -1.194 -0.324 C14 VDX 16
VDX C15 C15 C 0 1 N N N 12.661 24.266 36.350 0.510 -1.941 0.018 C15 VDX 17
VDX C16 C16 C 0 1 N N N 11.429 25.231 36.497 0.550 -2.003 1.571 C16 VDX 18
VDX C17 C17 C 0 1 N N R 11.276 25.934 35.106 1.445 -0.822 2.031 C17 VDX 19
VDX C18 C18 C 0 1 N N N 10.769 23.570 33.779 0.674 0.903 0.415 C18 VDX 20
VDX C19 C19 C 0 1 N N N 12.291 19.455 34.852 -0.938 -2.250 -4.026 C19 VDX 21
VDX C20 C20 C 0 1 N N R 9.849 26.546 34.726 0.672 0.090 2.985 C20 VDX 22
VDX C21 C21 C 0 1 N N N 9.804 27.956 35.482 1.548 1.283 3.370 C21 VDX 23
VDX C22 C22 C 0 1 N N N 8.575 25.824 35.268 0.293 -0.692 4.244 C22 VDX 24
VDX C23 C23 C 0 1 N N N 7.331 26.060 34.405 -0.479 0.220 5.198 C23 VDX 25
VDX C24 C24 C 0 1 N N N 6.152 25.266 34.672 -0.858 -0.561 6.457 C24 VDX 26
VDX C25 C25 C 0 1 N N N 4.775 25.776 34.336 -1.632 0.351 7.411 C25 VDX 27
VDX C26 C26 C 0 1 N N N 4.701 26.010 32.842 -2.010 -0.430 8.670 C26 VDX 28
VDX C27 C27 C 0 1 N N N 3.668 24.730 34.723 -0.756 1.545 7.796 C27 VDX 29
VDX O1 O1 O 0 1 N N N 13.119 17.359 36.620 -2.916 0.463 -4.127 O1 VDX 30
VDX HO2 HO2 H 0 1 N N N 17.695 18.454 34.260 -0.596 2.501 -7.662 HO2 VDX 31
VDX HO3 HO3 H 0 1 N N N 3.620 27.267 34.842 -3.340 0.037 6.540 HO3 VDX 32
VDX H11 1H1 H 0 1 N N N 14.859 18.417 36.467 -3.164 -1.374 -5.043 H11 VDX 33
VDX H21 1H2 H 0 1 N N N 15.307 16.086 35.534 -3.279 0.441 -6.756 H21 VDX 34
VDX H22 2H2 H 0 1 N N N 14.158 16.285 34.299 -2.003 -0.741 -7.125 H22 VDX 35
VDX H31 1H3 H 0 1 N N N 16.419 16.761 33.280 -1.535 1.892 -5.663 H31 VDX 36
VDX H41 1H4 H 0 1 N N N 16.145 19.140 32.402 0.842 1.386 -6.083 H41 VDX 37
VDX H42 2H4 H 0 1 N N N 14.714 18.239 32.256 0.388 -0.122 -6.917 H42 VDX 38
VDX H61 1H6 H 0 1 N N N 15.563 21.340 33.029 1.824 0.711 -4.042 H61 VDX 39
VDX H71 1H7 H 0 1 N N N 13.812 22.254 35.555 0.079 -1.340 -2.394 H71 VDX 40
VDX H91 1H9 H 0 1 N N N 15.184 24.670 32.555 3.938 -0.157 -1.954 H91 VDX 41
VDX H92 2H9 H 0 1 N N N 14.859 23.090 32.008 2.878 1.017 -2.763 H92 VDX 42
VDX H111 1H11 H 0 0 N N N 13.426 25.002 30.740 4.138 1.905 -0.747 H111 VDX 43
VDX H112 2H11 H 0 0 N N N 12.507 23.659 31.206 2.378 2.125 -0.700 H112 VDX 44
VDX H121 1H12 H 0 0 N N N 12.607 26.455 32.642 3.933 -0.085 0.727 H121 VDX 45
VDX H122 2H12 H 0 0 N N N 11.216 25.684 31.999 3.209 1.353 1.496 H122 VDX 46
VDX H141 1H14 H 0 0 N N N 13.932 25.330 34.753 2.667 -1.846 -0.206 H141 VDX 47
VDX H151 1H15 H 0 0 N N N 12.452 23.199 36.598 0.519 -2.944 -0.408 H151 VDX 48
VDX H152 2H15 H 0 0 N N N 13.457 24.403 37.117 -0.361 -1.383 -0.323 H152 VDX 49
VDX H161 1H16 H 0 0 N N N 10.500 24.721 36.845 0.982 -2.949 1.897 H161 VDX 50
VDX H162 2H16 H 0 0 N N N 11.517 25.942 37.350 -0.455 -1.890 1.976 H162 VDX 51
VDX H171 1H17 H 0 0 N N N 11.888 26.865 35.133 2.347 -1.197 2.514 H171 VDX 52
VDX H181 1H18 H 0 0 N N N 10.502 23.201 34.796 0.826 1.296 -0.589 H181 VDX 53
VDX H182 2H18 H 0 0 N N N 9.891 23.785 33.126 -0.282 0.384 0.461 H182 VDX 54
VDX H183 3H18 H 0 0 N N N 11.225 22.797 33.117 0.677 1.724 1.131 H183 VDX 55
VDX H191 1H19 H 0 0 N N N 11.563 18.992 35.539 0.042 -2.583 -3.722 H191 VDX 56
VDX H192 2H19 H 0 0 N N N 11.909 20.252 34.192 -1.795 -2.891 -3.879 H192 VDX 57
VDX H201 1H20 H 0 0 N N N 9.797 26.508 33.612 -0.232 0.446 2.492 H201 VDX 58
VDX H211 1H21 H 0 0 N N N 8.808 28.382 35.216 2.452 0.927 3.862 H211 VDX 59
VDX H212 2H21 H 0 0 N N N 9.993 27.890 36.578 1.818 1.841 2.473 H212 VDX 60
VDX H213 3H21 H 0 0 N N N 10.663 28.626 35.247 0.997 1.934 4.049 H213 VDX 61
VDX H221 1H22 H 0 0 N N N 8.764 24.733 35.400 -0.330 -1.542 3.969 H221 VDX 62
VDX H222 2H22 H 0 0 N N N 8.380 26.107 36.328 1.198 -1.048 4.736 H222 VDX 63
VDX H231 1H23 H 0 0 N N N 7.059 27.140 34.446 0.144 1.071 5.472 H231 VDX 64
VDX H232 2H23 H 0 0 N N N 7.607 25.950 33.330 -1.384 0.577 4.706 H232 VDX 65
VDX H241 1H24 H 0 0 N N N 6.283 24.275 34.176 -1.482 -1.411 6.182 H241 VDX 66
VDX H242 2H24 H 0 0 N N N 6.162 24.985 35.751 0.045 -0.918 6.949 H242 VDX 67
VDX H261 1H26 H 0 0 N N N 4.928 25.079 32.271 -2.561 0.220 9.350 H261 VDX 68
VDX H262 2H26 H 0 0 N N N 3.716 26.440 32.544 -2.634 -1.280 8.396 H262 VDX 69
VDX H263 3H26 H 0 0 N N N 5.360 26.852 32.527 -1.106 -0.787 9.162 H263 VDX 70
VDX H271 1H27 H 0 0 N N N 3.895 23.799 34.152 0.148 1.188 8.288 H271 VDX 71
VDX H272 2H27 H 0 0 N N N 3.584 24.563 35.822 -0.486 2.102 6.899 H272 VDX 72
VDX H273 3H27 H 0 0 N N N 2.630 25.105 34.559 -1.306 2.196 8.476 H273 VDX 73
VDX HO1 HO1 H 0 1 N N N 12.666 18.007 37.146 -2.988 0.050 -3.256 HO1 VDX 74
# #
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
VDX O2 C3 SING N N 1
VDX O2 HO2 SING N N 2
VDX O3 C25 SING N N 3
VDX O3 HO3 SING N N 4
VDX C1 C2 SING N N 5
VDX C1 C10 SING N N 6
VDX C1 O1 SING N N 7
VDX C1 H11 SING N N 8
VDX C2 C3 SING N N 9
VDX C2 H21 SING N N 10
VDX C2 H22 SING N N 11
VDX C3 C4 SING N N 12
VDX C3 H31 SING N N 13
VDX C4 C5 SING N N 14
VDX C4 H41 SING N N 15
VDX C4 H42 SING N N 16
VDX C5 C6 DOUB N Z 17
VDX C5 C10 SING N N 18
VDX C6 C7 SING N N 19
VDX C6 H61 SING N N 20
VDX C7 C8 DOUB N E 21
VDX C7 H71 SING N N 22
VDX C8 C9 SING N N 23
VDX C8 C14 SING N N 24
VDX C9 C11 SING N N 25
VDX C9 H91 SING N N 26
VDX C9 H92 SING N N 27
VDX C10 C19 DOUB N N 28
VDX C11 C12 SING N N 29
VDX C11 H111 SING N N 30
VDX C11 H112 SING N N 31
VDX C12 C13 SING N N 32
VDX C12 H121 SING N N 33
VDX C12 H122 SING N N 34
VDX C13 C14 SING N N 35
VDX C13 C17 SING N N 36
VDX C13 C18 SING N N 37
VDX C14 C15 SING N N 38
VDX C14 H141 SING N N 39
VDX C15 C16 SING N N 40
VDX C15 H151 SING N N 41
VDX C15 H152 SING N N 42
VDX C16 C17 SING N N 43
VDX C16 H161 SING N N 44
VDX C16 H162 SING N N 45
VDX C17 C20 SING N N 46
VDX C17 H171 SING N N 47
VDX C18 H181 SING N N 48
VDX C18 H182 SING N N 49
VDX C18 H183 SING N N 50
VDX C19 H191 SING N N 51
VDX C19 H192 SING N N 52
VDX C20 C21 SING N N 53
VDX C20 C22 SING N N 54
VDX C20 H201 SING N N 55
VDX C21 H211 SING N N 56
VDX C21 H212 SING N N 57
VDX C21 H213 SING N N 58
VDX C22 C23 SING N N 59
VDX C22 H221 SING N N 60
VDX C22 H222 SING N N 61
VDX C23 C24 SING N N 62
VDX C23 H231 SING N N 63
VDX C23 H232 SING N N 64
VDX C24 C25 SING N N 65
VDX C24 H241 SING N N 66
VDX C24 H242 SING N N 67
VDX C25 C26 SING N N 68
VDX C25 C27 SING N N 69
VDX C26 H261 SING N N 70
VDX C26 H262 SING N N 71
VDX C26 H263 SING N N 72
VDX C27 H271 SING N N 73
VDX C27 H272 SING N N 74
VDX C27 H273 SING N N 75
VDX O1 HO1 SING N N 76
# #
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
VDX SMILES ACDLabs 10.04 "OC3C(=C)/C(=C\C=C1/CCCC2(C)C(C(C)CCCC(O)(C)C)CCC12)CC(O)C3"
VDX SMILES_CANONICAL CACTVS 3.341 "C[C@H](CCCC(C)(C)O)[C@H]1CC[C@H]2C(/CCC[C@]12C)=C/C=C3/C[C@@H](O)C[C@H](O)C3=C"
VDX SMILES CACTVS 3.341 "C[CH](CCCC(C)(C)O)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C[CH](O)C3=C"
VDX SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[C@H](CCCC(C)(C)O)[C@H]1CC[C@@H]\2[C@@]1(CCC/C2=C\C=C/3\C[C@H](C[C@@H](C3=C)O)O)C"
VDX SMILES "OpenEye OEToolkits" 1.5.0 "CC(CCCC(C)(C)O)C1CCC2C1(CCCC2=CC=C3CC(CC(C3=C)O)O)C"
VDX InChI InChI 1.03 "InChI=1S/C27H44O3/c1-18(8-6-14-26(3,4)30)23-12-13-24-20(9-7-15-27(23,24)5)10-11-21-16-22(28)17-25(29)19(21)2/h10-11,18,22-25,28-30H,2,6-9,12-17H2,1,3-5H3/b20-10+,21-11-/t18-,22-,23-,24+,25+,27-/m1/s1"
VDX InChIKey InChI 1.03 GMRQFYUYWCNGIN-NKMMMXOESA-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
VDX "SYSTEMATIC NAME" ACDLabs 10.04 "(1S,3R,5Z,7E,14beta,17alpha)-9,10-secocholesta-5,7,10-triene-1,3,25-triol"
VDX "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(1R,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R)-6-hydroxy-6-methyl-heptan-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-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
VDX "Create component" 1999-11-03 PDBJ
VDX "Modify descriptor" 2011-06-04 RCSB
VDX "Modify synonyms" 2021-03-13 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id VDX
_pdbx_chem_comp_synonyms.name "1,25 DIHYDROXY VITAMIN D3"
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
##