Chemical Components in the PDB

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VD1 : Summary

Code

VD1

One-letter code

X

Molecule name

5-{2-[1-(1-METHYL-PROPYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYLENE-CYCLOHEXANE-1,3-DIOL

Synonyms

1-ALPHA-HYDROXY-2-METHYLENE-19-NOR-(20S)-BISHOMOPREGNACALCIFEROL
2MBISP

Systematic names

ProgramVersionName
ACDLabs 10.04 (1R,3R,7E,17beta)-2-methylidene-17-[(1S)-1-methylpropyl]-9,10-secoestra-5,7-diene-1,3-diol
OpenEye OEToolkits 1.5.0 (1R,3R)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2S)-butan-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol

Formula

C23 H36 O2

Formal charge

0

Molecular weight

344.531 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 OC3\C(=C)C(O)CC(=C\C=C1/CCCC2(C1CCC2C(C)CC)C)\C3
SMILES CACTVS 3.385 CC[CH](C)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C(=C)[CH](O)C3
SMILES OpenEye OEToolkits 1.7.5 CCC(C)C1CCC2C1(CCCC2=CC=C3CC(C(=C)C(C3)O)O)C
Canonical SMILES CACTVS 3.385 CC[C@H](C)[C@H]1CC[C@H]2C(/CCC[C@]12C)=C/C=C3C[C@@H](O)C(=C)[C@H](O)C3
Canonical SMILES OpenEye OEToolkits 1.7.5 CC[C@H](C)[C@H]1CC[C@@H]\2[C@@]1(CCC/C2=C\C=C3C[C@H](C(=C)[C@@H](C3)O)O)C

IUPAC InChI

InChI=1S/C23H36O2/c1-5-15(2)19-10-11-20-18(7-6-12-23(19,20)4)9-8-17-13-21(24)16(3)22(25)14-17/h8-9,15,19-22,24-25H,3,5-7,10-14H2,1-2,4H3/b18-9+/t15-,19+,20-,21+,22+,23+/m0/s1

IUPAC InChI key

QSLUXQQUPXBIHH-YHSKWIAJSA-N
VD1

wwPDB Information

Atom count

61 (25 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2003-12-17

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



VD1 : Atoms of Molecule

Total Number of Atoms: 61
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O2 O O2 N N N 0 5.251 -1.514 -0.87
2 C3 C C3 R N N 0 5.276 -0.983 0.456
3 C2 C C2 N N N 0 5.439 0.519 0.399
4 C28 C C28 N N N 0 6.512 1.092 0.884
5 C1 C C1 R N N 0 4.341 1.347 -0.228
6 O1 O O1 N N N 0 4.641 2.736 -0.075
7 C4 C C4 N N N 0 3.954 -1.306 1.165
8 C5 C C5 N N N 0 2.856 -0.477 0.538
9 C10 C C10 N N N 0 3.019 1.025 0.481
10 C6 C C6 N N N 0 1.768 -1.058 0.045
11 C7 C C7 N N N 0 0.651 -0.235 -0.442
12 C8 C C8 N N N 0 -0.478 -0.813 -0.838
13 C9 C C9 N N N 0 -0.674 -2.322 -0.81
14 C11 C C11 N N N 0 -1.983 -2.684 -0.11
15 C12 C C12 N N N 0 -3.163 -1.853 -0.642
16 C13 C C13 R N N 0 -2.836 -0.397 -0.409
17 C18 C C18 N N N 0 -2.408 -0.201 1.047
18 C14 C C14 S N N 0 -1.652 -0.025 -1.339
19 C15 C C15 N N N 0 -1.592 1.492 -1.15
20 C17 C C17 R N N 0 -3.884 0.645 -0.769
21 C16 C C16 N N N 0 -3.093 1.899 -1.166
22 C20 C C20 S N N 0 -4.759 0.96 0.445
23 C21 C C21 N N N 0 -5.805 2.009 0.062
24 C22 C C22 N N N 0 -5.463 -0.316 0.911
25 C23 C C23 N N N 0 -6.24 -0.029 2.198
26 HO2 H HO2 N N N 0 6.052 -1.334 -1.381
27 H3 H H3 N N N 0 6.107 -1.42 1.01
28 H281 H 1H28 N N N 0 7.291 0.491 1.329
29 H282 H 2H28 N N N 0 6.619 2.166 0.838
30 H1 H H1 N N N 0 4.259 1.106 -1.288
31 HO1 H HO1 N N N 0 5.472 3.007 -0.488
32 H41 H 1H4 N N N 0 3.725 -2.365 1.048
33 H42 H 2H4 N N N 0 4.038 -1.061 2.224
34 H101 H 1H10 N N N 0 3.038 1.43 1.492
35 H102 H 2H10 N N N 0 2.19 1.462 -0.075
36 H6 H H6 N N N 0 1.703 -2.135 0.003
37 H7 H H7 N N N 0 0.748 0.84 -0.479
38 H91 H 1H9 N N N 0 -0.697 -2.7 -1.832
39 H92 H 2H9 N N N 0 0.157 -2.782 -0.276
40 H111 H 1H11 N N N 0 -2.191 -3.741 -0.272
41 H112 H 2H11 N N N 0 -1.875 -2.504 0.96
42 H121 H 1H12 N N N 0 -3.294 -2.037 -1.708
43 H122 H 2H12 N N N 0 -4.074 -2.118 -0.105
44 H181 H 1H18 N N N 0 -1.535 -0.819 1.256
45 H182 H 2H18 N N N 0 -2.16 0.847 1.215
46 H183 H 3H18 N N N 0 -3.225 -0.491 1.708
47 H14 H H14 N N N 0 -1.877 -0.284 -2.373
48 H151 H 1H15 N N N 0 -1.134 1.744 -0.193
49 H152 H 2H15 N N N 0 -1.055 1.963 -1.973
50 H17 H H17 N N N 0 -4.497 0.294 -1.599
51 H161 H 1H16 N N N 0 -3.269 2.71 -0.459
52 H162 H 2H16 N N N 0 -3.386 2.208 -2.17
53 H20 H H20 N N N 0 -4.136 1.346 1.252
54 H211 H 1H21 N N N 0 -6.429 2.233 0.927
55 H222 H 2H22 N N N 0 -4.721 -1.092 1.1
56 H212 H 2H21 N N N 0 -5.304 2.918 -0.27
57 H213 H 3H21 N N N 0 -6.428 1.622 -0.745
58 H221 H 1H22 N N N 0 -6.153 -0.653 0.138
59 H231 H 1H23 N N N 0 -5.549 0.308 2.971
60 H232 H 2H23 N N N 0 -6.981 0.747 2.01
61 H233 H 3H23 N N N 0 -6.741 -0.938 2.53



VD1 : Chemical Bonds

Total Number of Bonds: 63
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O2 C3 O C sing 1.43 N N
2 O2 HO2 O H sing 0.97 N N
3 C3 C2 C C sing 1.51 N N
4 C3 C4 C C sing 1.53 N N
5 C3 H3 C H sing 1.09 N N
6 C2 C28 C C doub 1.31 N N
7 C2 C1 C C sing 1.51 N N
8 C28 H281 C H sing 1.08 N N
9 C28 H282 C H sing 1.08 N N
10 C1 O1 C O sing 1.43 N N
11 C1 C10 C C sing 1.53 N N
12 C1 H1 C H sing 1.09 N N
13 O1 HO1 O H sing 0.97 N N
14 C4 C5 C C sing 1.51 N N
15 C4 H41 C H sing 1.09 N N
16 C4 H42 C H sing 1.09 N N
17 C5 C10 C C sing 1.51 N N
18 C5 C6 C C doub 1.33 N N
19 C10 H101 C H sing 1.09 N N
20 C10 H102 C H sing 1.09 N N
21 C6 C7 C C sing 1.47 N N
22 C6 H6 C H sing 1.08 N N
23 C7 C8 C C doub 1.33 E N
24 C7 H7 C H sing 1.08 N N
25 C8 C9 C C sing 1.52 N N
26 C8 C14 C C sing 1.5 N N
27 C9 C11 C C sing 1.53 N N
28 C9 H91 C H sing 1.09 N N
29 C9 H92 C H sing 1.09 N N
30 C11 C12 C C sing 1.54 N N
31 C11 H111 C H sing 1.09 N N
32 C11 H112 C H sing 1.09 N N
33 C12 C13 C C sing 1.51 N N
34 C12 H121 C H sing 1.09 N N
35 C12 H122 C H sing 1.09 N N
36 C13 C18 C C sing 1.53 N N
37 C13 C14 C C sing 1.55 N N
38 C13 C17 C C sing 1.52 N N
39 C18 H181 C H sing 1.09 N N
40 C18 H182 C H sing 1.09 N N
41 C18 H183 C H sing 1.09 N N
42 C14 C15 C C sing 1.53 N N
43 C14 H14 C H sing 1.09 N N
44 C15 C16 C C sing 1.56 N N
45 C15 H151 C H sing 1.09 N N
46 C15 H152 C H sing 1.09 N N
47 C17 C16 C C sing 1.53 N N
48 C17 C20 C C sing 1.53 N N
49 C17 H17 C H sing 1.09 N N
50 C16 H161 C H sing 1.09 N N
51 C16 H162 C H sing 1.09 N N
52 C20 C21 C C sing 1.53 N N
53 C20 C22 C C sing 1.53 N N
54 C20 H20 C H sing 1.09 N N
55 C21 H211 C H sing 1.09 N N
56 C21 H212 C H sing 1.09 N N
57 C21 H213 C H sing 1.09 N N
58 C22 C23 C C sing 1.53 N N
59 C22 H221 C H sing 1.09 N N
60 C22 H222 C H sing 1.09 N N
61 C23 H231 C H sing 1.09 N N
62 C23 H232 C H sing 1.09 N N
63 C23 H233 C H sing 1.09 N N



VD1 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
VD1 1rkg Open in New Window Bound ligand 1 1