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.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_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 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 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 N N N 14.139 17.953 35.755 -2.455 -0.546 -5.027 C1 VDX 3
VDX C2 C2 C 0 1 N N N 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 N N N 15.992 17.534 33.962 -1.276 1.161 -6.429 C3 VDX 5
VDX C4 C4 C 0 1 N N N 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 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 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 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 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 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 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 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 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 N N N 11.753 24.897 34.070 1.801 -0.074 0.756 C13 VDX 15
VDX C14 C14 C 0 1 N N S N N N 13.148 24.538 34.777 1.801 -1.194 -0.324 C14 VDX 16
VDX C15 C15 C 0 1 N N N 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 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 N N N 11.276 25.934 35.106 1.445 -0.822 2.031 C17 VDX 19
VDX C18 C18 C 0 1 N N N 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 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 N N N 9.849 26.546 34.726 0.672 0.090 2.985 C20 VDX 22
VDX C21 C21 C 0 1 N N N 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 ?
#
_pdbe_chem_comp_drugbank_details.comp_id VDX
_pdbe_chem_comp_drugbank_details.drugbank_id DB00136
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Calcitriol
_pdbe_chem_comp_drugbank_details.description
'Calcitriol is an active metabolite of vitamin D with 3 hydroxyl (OH) groups and is commonly referred to as 1,25-dihydroxycholecalciferol, or 1alpha,25-dihydroxyvitamin D<sub>3</sub>, 1,25-dihydroxyvitamin D<sub>3</sub>. It is produced in the body after series of conversion steps of 7-dehydrocholesterol from exposure to UV light. 7-dehydrocholesterol is converted to [DB00169] (vitamin D3) in the skin, which is then converted to [DB00146] in the liver and kidneys. [DB00146] undergoes hydroxylation to form calcitriol via 1α-hydroxylase (CYP27B1) activity [A26353]. Calcitriol is considered to be the most potent metabolite of vitamin D in humans [A3366]. Renal production of calcitriol is stimulated in response to PTH, low calcium and low phosphate [A26353]. Calcitriol plays a role in plasma calcium regulation in concert with parathyroid hormone (PTH) by enhancing absorption of dietary calcium and phosphate from the gastrointestinal tract, promoting renal tubular reabsorption of calcium in the kidneys, and stimulating the release of calcium stores from the skeletal system. In addition to promoting fatty acid synthesis and inhibiting lipolysis, calcitriol has been demonstrated to increase energy efficiency by suppressing UCP2 expression, which is modulated by signaling pathways of classical nuclear receptors (nVDR), where calcitriol acts as a natural ligand [A175615]. There is also evidence that calcitriol modulates the action of cytokines and may regulate immune and inflammatory response, cell turnover, cell differentiation [A26353].   Administered orally and intravenously, calcitriol is commonly used as a medication in the treatment of secondary hyperparathyroidism and resultant metabolic bone disease, hypocalcemia in patients undergoing chronic renal dialysis, and osteoporosis. It is also available in topical form for the treatment of mild to moderate plaque psoriasis in adults. Calcitriol is marketed under various trade names including Rocaltrol (Roche), Calcijex (Abbott) and Decostriol (Mibe, Jesalis).'
_pdbe_chem_comp_drugbank_details.cas_number 32222-06-3
_pdbe_chem_comp_drugbank_details.mechanism_of_action
'The mechanism of action of calcitriol in the treatment of psoriasis is accounted for by their antiproliferative activity for keratinocytes and their stimulation of epidermal cell differentiation. The anticarcinogenic activity of the active form of Calcitriol appears to be correlated with cellular vitamin D receptor (VDR) levels. Vitamin D receptors belong to the superfamily of steroid-hormone zinc-finger receptors. VDRs selectively bind 1,25-(OH)<sub>2</sub>-D3 and retinoic acid X receptor (RXR) to form a heterodimeric complex that interacts with specific DNA sequences known as vitamin D-responsive elements. VDRs are ligand-activated transcription factors. The receptors activate or repress the transcription of target genes upon binding their respective ligands. It is thought that the anticarcinogenic effect of Calcitriol is mediated via VDRs in cancer cells. The immunomodulatory activity of calcitriol is thought to be mediated by vitamin D receptors (VDRs) which are expressed constitutively in monocytes but induced upon activation of T and B lymphocytes. 1,25-(OH)<sub>2</sub>-D3 has also been found to enhance the activity of some vitamin D-receptor positive immune cells and to enhance the sensitivity of certain target cells to various cytokines secreted by immune cells.  A study suggests that calcitriol plays an immunoregulatry role by suppressing the aryl hydrocarbon receptor (AhR) expression in human Th9, a pro-inflammatory CD4 T cell subset [A175747]. This suppression subsequently leads to repressed expression of BATF, a transcription factor essential for Th9 [A175747]. Calcitriol has also been found to induce monocyte differentiation and to inhibit lymphocyte proliferation and production of cytokines, including interleukin IL-1 and IL-2, as well as to suppress immunoglobulin secretion by B lymphocytes.'
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
VDX '1,25 DIHYDROXY VITAMIN D3' wwPDB ?
VDX (1S,3R,5Z,7E)-9,10-secocholesta-5,7,10-triene-1,3,25-triol DrugBank ?
VDX '(1α,3β,5Z,7E)-9,10-secocholesta-5,7,10(19)-triene-1,3,25-triol' DrugBank ?
VDX (5Z,7E)-(1S,3R)-9,10-secocholesta-5,7,10(19)-triene-1,3,25-triol DrugBank ?
VDX '1-alpha-25-Dihydroxyvitamin D3' DrugBank ?
VDX 1,25-DHCC DrugBank ?
VDX 1,25-dihydroxycholecalciferol DrugBank ?
VDX '1α,25-dihydroxycholecalciferol' DrugBank ?
VDX '1α,25-dihydroxyvitamin D3' DrugBank ?
VDX '1α,25(OH)2D3' DrugBank ?
VDX Calcitriol DrugBank ?
VDX Calcitriolum DrugBank ?
VDX Asentar DrugBank 'International brand'
VDX 'Calcitriol Oral Solution' DrugBank 'International brand'
VDX Decostriol DrugBank 'International brand'
#
_pdbe_chem_comp_drugbank_classification.comp_id VDX
_pdbe_chem_comp_drugbank_classification.drugbank_id DB00136
_pdbe_chem_comp_drugbank_classification.parent 'Vitamin D and derivatives'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Steroids and steroid derivatives'
_pdbe_chem_comp_drugbank_classification.superclass 'Lipids and lipid-like molecules'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as vitamin d and derivatives. These are compounds containing a secosteroid backbone, usually secoergostane or secocholestane.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
VDX DB00136 'Vitamin D3 receptor' Humans P11473 yes 1
VDX DB00136 'Homeobox protein Hox-A10' Humans P31260 unknown 2
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
VDX O2 O 3.000 -7.520 1
VDX O3 O 14.415 8.258 2
VDX C1 C 6.897 -6.770 3
VDX C2 C 5.598 -7.520 4
VDX C3 C 4.299 -6.770 5
VDX C4 C 4.299 -5.270 6
VDX C5 C 5.598 -4.520 7
VDX C6 C 5.598 -3.020 8
VDX C7 C 6.897 -2.270 9
VDX C8 C 6.897 -0.770 10
VDX C9 C 5.598 -0.020 11
VDX C10 C 6.897 -5.270 12
VDX C11 C 5.598 1.480 13
VDX C12 C 6.897 2.230 14
VDX C13 C 8.196 1.480 15
VDX C14 C 8.196 -0.020 16
VDX C15 C 9.616 -0.477 17
VDX C16 C 10.491 0.730 18
VDX C17 C 9.616 1.937 19
VDX C18 C 8.196 2.980 20
VDX C19 C 8.196 -4.520 21
VDX C20 C 10.082 3.362 22
VDX C21 C 9.080 4.479 23
VDX C22 C 11.549 3.672 24
VDX C23 C 12.015 5.098 25
VDX C24 C 13.483 5.407 26
VDX C25 C 13.949 6.833 27
VDX C26 C 15.375 6.367 28
VDX C27 C 12.523 7.299 29
VDX O1 O 8.196 -7.520 30
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
VDX C3 O2 SINGLE BEGINDASH 1
VDX O3 C25 SINGLE NONE 2
VDX C1 C2 SINGLE NONE 3
VDX C1 C10 SINGLE NONE 4
VDX C1 O1 SINGLE BEGINWEDGE 5
VDX C2 C3 SINGLE NONE 6
VDX C3 C4 SINGLE NONE 7
VDX C4 C5 SINGLE ENDUPRIGHT 8
VDX C5 C6 DOUBLE NONE 9
VDX C5 C10 SINGLE ENDUPRIGHT 10
VDX C6 C7 SINGLE ENDUPRIGHT 11
VDX C7 C8 DOUBLE NONE 12
VDX C8 C9 SINGLE ENDDOWNRIGHT 13
VDX C8 C14 SINGLE ENDUPRIGHT 14
VDX C9 C11 SINGLE NONE 15
VDX C10 C19 DOUBLE NONE 16
VDX C11 C12 SINGLE NONE 17
VDX C12 C13 SINGLE NONE 18
VDX C13 C14 SINGLE NONE 19
VDX C13 C17 SINGLE NONE 20
VDX C13 C18 SINGLE BEGINWEDGE 21
VDX C14 C15 SINGLE NONE 22
VDX C15 C16 SINGLE NONE 23
VDX C17 C16 SINGLE BEGINWEDGE 24
VDX C17 C20 SINGLE NONE 25
VDX C20 C21 SINGLE BEGINDASH 26
VDX C20 C22 SINGLE NONE 27
VDX C22 C23 SINGLE NONE 28
VDX C23 C24 SINGLE NONE 29
VDX C24 C25 SINGLE NONE 30
VDX C25 C26 SINGLE NONE 31
VDX C25 C27 SINGLE NONE 32
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
VDX MurckoScaffold S1 scaffold 'C=C1CCCC/C1=C/C=C1\CCCC2CCC[C@@H]12' InChI=1S/C18H26/c1-14-6-2-3-7-15(14)12-13-17-9-4-8-16-10-5-11-18(16)17/h12-13,16,18H,1-11H2/b15-12-,17-13+/t16-,18-/m1/s1 GBDZMYYBUXFGPL-VDTWJZRYSA-N
VDX cyclohexane F1 fragment C1CCCCC1 InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2 XDTMQSROBMDMFD-UHFFFAOYSA-N
VDX cyclopentane F2 fragment C1CCCC1 InChI=1S/C5H10/c1-2-4-5-3-1/h1-5H2 RGSFGYAAUTVSQA-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
VDX C1 S1 1
VDX C2 S1 1
VDX C3 S1 1
VDX C4 S1 1
VDX C5 S1 1
VDX C6 S1 1
VDX C7 S1 1
VDX C8 S1 1
VDX C9 S1 1
VDX C10 S1 1
VDX C11 S1 1
VDX C12 S1 1
VDX C13 S1 1
VDX C14 S1 1
VDX C15 S1 1
VDX C16 S1 1
VDX C17 S1 1
VDX C19 S1 1
VDX C1 F1 1
VDX C2 F1 1
VDX C3 F1 1
VDX C4 F1 1
VDX C5 F1 1
VDX C10 F1 1
VDX C8 F1 2
VDX C9 F1 2
VDX C11 F1 2
VDX C12 F1 2
VDX C13 F1 2
VDX C14 F1 2
VDX C13 F2 1
VDX C14 F2 1
VDX C15 F2 1
VDX C16 F2 1
VDX C17 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id VDX
_pdbe_chem_comp_rdkit_properties.exactmw 416.329
_pdbe_chem_comp_rdkit_properties.amw 416.646
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 13
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 30
_pdbe_chem_comp_rdkit_properties.NumAtoms 74
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.778
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 3
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 3
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 6
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 245.603
_pdbe_chem_comp_rdkit_properties.tpsa 60.690
_pdbe_chem_comp_rdkit_properties.CrippenClogP 5.705
_pdbe_chem_comp_rdkit_properties.CrippenMR 124.038
_pdbe_chem_comp_rdkit_properties.chi0v 14.725
_pdbe_chem_comp_rdkit_properties.chi1v 7.862
_pdbe_chem_comp_rdkit_properties.chi2v 3.681
_pdbe_chem_comp_rdkit_properties.chi3v 3.681
_pdbe_chem_comp_rdkit_properties.chi4v 2.356
_pdbe_chem_comp_rdkit_properties.chi0n 58.725
_pdbe_chem_comp_rdkit_properties.chi1n 29.587
_pdbe_chem_comp_rdkit_properties.chi2n 3.681
_pdbe_chem_comp_rdkit_properties.chi3n 3.681
_pdbe_chem_comp_rdkit_properties.chi4n 2.356
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.900
_pdbe_chem_comp_rdkit_properties.kappa1 4.074
_pdbe_chem_comp_rdkit_properties.kappa2 9.303
_pdbe_chem_comp_rdkit_properties.kappa3 5.285
_pdbe_chem_comp_rdkit_properties.Phi 1.263
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
VDX UniChem DrugBank DB00136
VDX UniChem 'Guide to Pharmacology' 2779
VDX UniChem 'PubChem DOTF' 12012574
VDX UniChem 'KEGG LIGAND' C01673
VDX UniChem ChEBI 17823
VDX UniChem NIH SAM001246772
VDX UniChem ZINC ZINC000100015048
VDX UniChem atlas '1,25-dihydroxyvitamin D3'
VDX UniChem atlas '1alpha,25-Dihydroxyvitamin D3'
VDX UniChem fdasrs FXC9231JVH
VDX UniChem HMDB HMDB0001903
VDX UniChem Selleck Calcitriol-(Rocaltrol)
VDX UniChem PubChem 5280453
VDX UniChem NMRShiftDB 60020500
VDX UniChem LINCS LSM-43088
VDX UniChem BindingDb 50200182
VDX UniChem LipidMaps LMST03020258
VDX UniChem DrugCentral 466
VDX UniChem MetaboLights MTBLC17823
VDX UniChem BRENDA 102023
VDX UniChem BRENDA 12463
VDX UniChem BRENDA 163402
VDX UniChem BRENDA 168069
VDX UniChem BRENDA 1953
VDX UniChem BRENDA 199247
VDX UniChem BRENDA 84138
VDX UniChem BRENDA 86868
VDX UniChem Rhea 17823
VDX UniChem DailyMed CALCITRIOL
VDX UniChem ClinicalTrials CALCIJEX
VDX UniChem ClinicalTrials CALCITRIOL
VDX UniChem ClinicalTrials 'RO 21-5535'
VDX UniChem ClinicalTrials RO-21-5535
VDX UniChem ClinicalTrials ROCALTROL
VDX UniChem ClinicalTrials VECTICAL
VDX UniChem rxnorm CALCITRIOL
VDX UniChem rxnorm ROCALTROL
VDX UniChem rxnorm VECTICAL
VDX UniChem MedChemExpress HY-10002
VDX UniChem 'Probes And Drugs' PD003123
VDX UniChem CCDC HIJFAH
VDX UniChem eMolecules 29541527
VDX UniChem eMolecules 485907
VDX UniChem SureChEMBL SCHEMBL3245
VDX UniChem 'PubChem TPHARMA' 14758022
VDX UniChem 'PubChem TPHARMA' 14855739
VDX UniChem ACTor 32222-06-3
VDX UniChem Recon 1a25dhvitd3
VDX UniChem Nikkaji J17.427K
VDX UniChem 'EPA CompTox Dashboard' DTXSID5022722
VDX UniChem BRENDA 156164
VDX UniChem BRENDA 168065
VDX UniChem SwissLipids SLM:000000475
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
VDX O2 8.912 1.117 -1.337 ETKDGv3 1
VDX O3 -8.092 -0.747 -1.438 ETKDGv3 2
VDX C1 5.828 0.392 -3.415 ETKDGv3 3
VDX C2 7.325 0.501 -3.065 ETKDGv3 4
VDX C3 7.541 0.980 -1.614 ETKDGv3 5
VDX C4 6.877 0.025 -0.604 ETKDGv3 6
VDX C5 5.422 -0.187 -0.946 ETKDGv3 7
VDX C6 4.492 -0.160 0.031 ETKDGv3 8
VDX C7 3.036 -0.157 -0.232 ETKDGv3 9
VDX C8 2.101 -0.571 0.649 ETKDGv3 10
VDX C9 2.434 -1.321 1.931 ETKDGv3 11
VDX C10 5.109 -0.440 -2.380 ETKDGv3 12
VDX C11 1.452 -1.007 3.080 ETKDGv3 13
VDX C12 -0.033 -0.977 2.647 ETKDGv3 14
VDX C13 -0.249 -0.054 1.417 ETKDGv3 15
VDX C14 0.631 -0.607 0.285 ETKDGv3 16
VDX C15 0.120 0.078 -0.974 ETKDGv3 17
VDX C16 -1.388 0.223 -0.732 ETKDGv3 18
VDX C17 -1.657 -0.144 0.753 ETKDGv3 19
VDX C18 0.116 1.424 1.766 ETKDGv3 20
VDX C19 4.280 -1.422 -2.756 ETKDGv3 21
VDX C20 -2.824 0.704 1.376 ETKDGv3 22
VDX C21 -3.110 0.338 2.843 ETKDGv3 23
VDX C22 -4.138 0.634 0.544 ETKDGv3 24
VDX C23 -4.856 -0.730 0.587 ETKDGv3 25
VDX C24 -5.849 -0.956 -0.576 ETKDGv3 26
VDX C25 -7.156 -0.099 -0.607 ETKDGv3 27
VDX C26 -6.903 1.284 -1.235 ETKDGv3 28
VDX C27 -7.778 0.082 0.795 ETKDGv3 29
VDX O1 5.242 1.668 -3.454 ETKDGv3 30
VDX HO2 9.331 0.223 -1.445 ETKDGv3 31
VDX HO3 -8.354 -1.603 -1.007 ETKDGv3 32
VDX H11 5.744 -0.085 -4.420 ETKDGv3 33
VDX H21 7.802 -0.495 -3.203 ETKDGv3 34
VDX H22 7.819 1.208 -3.765 ETKDGv3 35
VDX H31 7.076 1.985 -1.502 ETKDGv3 36
VDX H41 6.997 0.451 0.416 ETKDGv3 37
VDX H42 7.389 -0.962 -0.622 ETKDGv3 38
VDX H61 4.829 -0.021 1.049 ETKDGv3 39
VDX H71 2.721 0.217 -1.196 ETKDGv3 40
VDX H91 3.455 -1.110 2.302 ETKDGv3 41
VDX H92 2.387 -2.410 1.711 ETKDGv3 42
VDX H111 1.576 -1.773 3.876 ETKDGv3 43
VDX H112 1.725 -0.032 3.538 ETKDGv3 44
VDX H121 -0.631 -0.638 3.513 ETKDGv3 45
VDX H122 -0.358 -2.014 2.412 ETKDGv3 46
VDX H141 0.396 -1.691 0.144 ETKDGv3 47
VDX H151 0.579 1.083 -1.095 ETKDGv3 48
VDX H152 0.327 -0.535 -1.879 ETKDGv3 49
VDX H161 -1.682 1.273 -0.952 ETKDGv3 50
VDX H162 -1.958 -0.456 -1.404 ETKDGv3 51
VDX H171 -1.956 -1.215 0.779 ETKDGv3 52
VDX H181 -0.407 1.751 2.687 ETKDGv3 53
VDX H182 1.203 1.555 1.940 ETKDGv3 54
VDX H183 -0.164 2.120 0.949 ETKDGv3 55
VDX H191 3.811 -2.071 -2.027 ETKDGv3 56
VDX H192 4.074 -1.609 -3.803 ETKDGv3 57
VDX H201 -2.521 1.773 1.362 ETKDGv3 58
VDX H211 -3.141 -0.764 2.978 ETKDGv3 59
VDX H212 -4.083 0.761 3.172 ETKDGv3 60
VDX H213 -2.345 0.775 3.513 ETKDGv3 61
VDX H221 -3.942 0.924 -0.508 ETKDGv3 62
VDX H222 -4.826 1.399 0.959 ETKDGv3 63
VDX H231 -4.108 -1.544 0.516 ETKDGv3 64
VDX H232 -5.364 -0.865 1.564 ETKDGv3 65
VDX H241 -6.144 -2.027 -0.517 ETKDGv3 66
VDX H242 -5.307 -0.854 -1.542 ETKDGv3 67
VDX H261 -6.383 1.181 -2.211 ETKDGv3 68
VDX H262 -7.872 1.797 -1.420 ETKDGv3 69
VDX H263 -6.306 1.944 -0.579 ETKDGv3 70
VDX H271 -8.778 0.559 0.710 ETKDGv3 71
VDX H272 -7.905 -0.903 1.294 ETKDGv3 72
VDX H273 -7.145 0.729 1.438 ETKDGv3 73
VDX HO1 5.550 2.100 -4.293 ETKDGv3 74
#