Chemical Components in the PDB

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TOK : Summary

Code

TOK

One-letter code

X

Molecule name

(3alpha,8alpha)-17-(1H-benzimidazol-1-yl)androsta-5,16-dien-3-ol

Systematic names

ProgramVersionName
ACDLabs 12.01 (3alpha,8alpha)-17-(1H-benzimidazol-1-yl)androsta-5,16-dien-3-ol
OpenEye OEToolkits 1.7.2 (3S,8R,9S,10R,13S,14S)-17-(benzimidazol-1-yl)-10,13-dimethyl-2,3,4,7,8,9,11,12,14,15-decahydro-1H-cyclopenta[a]phenanthren-3-ol

Formula

C26 H32 N2 O

Formal charge

0

Molecular weight

388.545 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 n2c1ccccc1n(c2)C4=CCC5C6CC=C3CC(O)CCC3(C)C6CCC45C
SMILES CACTVS 3.370 C[C]12CC[CH](O)CC1=CC[CH]3[CH]2CC[C]4(C)[CH]3CC=C4n5cnc6ccccc56
SMILES OpenEye OEToolkits 1.7.2 CC12CCC(CC1=CCC3C2CCC4(C3CC=C4n5cnc6c5cccc6)C)O
Canonical SMILES CACTVS 3.370 C[C@]12CC[C@H](O)CC1=CC[C@@H]3[C@@H]2CC[C@@]4(C)[C@H]3CC=C4n5cnc6ccccc56
Canonical SMILES OpenEye OEToolkits 1.7.2 C[C@]12CC[C@@H](CC1=CC[C@@H]3[C@@H]2CC[C@]4([C@H]3CC=C4n5cnc6c5cccc6)C)O

IUPAC InChI

InChI=1S/C26H32N2O/c1-25-13-11-18(29)15-17(25)7-8-19-20-9-10-24(26(20,2)14-12-21(19)25)28-16-27-22-5-3-4-6-23(22)28/h3-7,10,16,18-21,29H,8-9,11-15H2,1-2H3/t18-,19-,20-,21-,25-,26-/m0/s1

IUPAC InChI key

PAFKTGFSEFKSQG-PAASFTFBSA-N
TOK

wwPDB Information

Atom count

61 (29 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2011-08-08

Last modified at

2012-01-20

Status

Released

Obsoleted

Not Assigned



TOK : 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 C1 C C1 N N N 0 -3.993 1.571 -0.735
2 C2 C C2 N N N 0 -5.344 1.872 -0.084
3 C3 C C3 S N N 0 -6.21 0.61 -0.087
4 O3 O O3 N N N 0 -7.501 0.918 0.441
5 C4 C C4 N N N 0 -5.547 -0.465 0.779
6 C5 C C5 N N N 0 -4.132 -0.686 0.27
7 C6 C C6 N N N 0 -3.753 -1.905 0.016
8 C7 C C7 N N N 0 -2.384 -2.245 -0.497
9 C8 C C8 R N N 0 -1.394 -1.163 -0.053
10 C9 C C9 S N N 0 -1.915 0.194 -0.55
11 C10 C C10 R N N 0 -3.253 0.516 0.093
12 C11 C C11 N N N 0 -0.928 1.326 -0.282
13 C12 C C12 N N N 0 0.477 1.008 -0.821
14 C13 C C13 S N N 0 0.904 -0.293 -0.182
15 C14 C C14 S N N 0 -0.051 -1.4 -0.718
16 C15 C C15 N N N 0 0.746 -2.621 -0.239
17 C16 C C16 N N N 0 2.185 -2.175 -0.501
18 C17 C C17 N N N 0 2.257 -0.843 -0.484
19 C18 C C18 N N N 0 0.728 -0.192 1.334
20 C19 C C19 N N N 0 -2.972 1.109 1.475
21 N48 N N48 N Y N 0 3.408 -0.09 -0.711
22 C49 C C49 N Y N 0 4.463 0.082 0.167
23 C50 C C50 N Y N 0 5.385 0.913 -0.492
24 N51 N N51 N Y N 0 4.859 1.202 -1.71
25 C52 C C52 N Y N 0 3.706 0.611 -1.842
26 C53 C C53 N Y N 0 4.739 -0.377 1.447
27 C54 C C54 N Y N 0 5.916 -0.012 2.065
28 C55 C C55 N Y N 0 6.826 0.81 1.414
29 C56 C C56 N Y N 0 6.572 1.27 0.153
30 H1 H H1 N N N 0 -4.152 1.194 -1.745
31 H1A H H1A N N N 0 -3.398 2.483 -0.777
32 H2 H H2 N N N 0 -5.187 2.201 0.943
33 H2A H H2A N N N 0 -5.85 2.659 -0.644
34 H3 H H3 N N N 0 -6.312 0.243 -1.108
35 HO3 H HO3 N N N 0 -8.105 0.162 0.469
36 H4 H H4 N N N 0 -5.515 -0.133 1.817
37 H4A H H4A N N N 0 -6.112 -1.394 0.707
38 H6 H H6 N N N 0 -4.455 -2.708 0.184
39 H7 H H7 N N N 0 -2.074 -3.209 -0.094
40 H7A H H7A N N N 0 -2.406 -2.295 -1.586
41 H8 H H8 N N N 0 -1.286 -1.17 1.031
42 H9 H H9 N N N 0 -2.073 0.126 -1.627
43 H11 H H11 N N N 0 -1.294 2.235 -0.761
44 H11A H H11A N N N 0 -0.866 1.494 0.793
45 H12 H H12 N N N 0 0.444 0.897 -1.905
46 H12A H H12A N N N 0 1.17 1.804 -0.549
47 H14 H H14 N N N 0 -0.137 -1.366 -1.804
48 H15 H H15 N N N 0 0.581 -2.803 0.823
49 H16 H H16 N N N 0 3.018 -2.84 -0.675
50 H18 H H18 N N N 0 -0.298 0.099 1.562
51 H18A H H18A N N N 0 0.94 -1.159 1.79
52 H18B H H18B N N N 0 1.414 0.555 1.731
53 H19 H H19 N N N 0 -2.352 0.418 2.047
54 H19A H H19A N N N 0 -2.449 2.059 1.364
55 H19B H H19B N N N 0 -3.914 1.271 1.999
56 H52 H H52 N N N 0 3.077 0.67 -2.717
57 H53 H H53 N N N 0 4.034 -1.016 1.958
58 H54 H H54 N N N 0 6.132 -0.367 3.062
59 H55 H H55 N N N 0 7.745 1.088 1.91
60 H56 H H56 N N N 0 7.287 1.909 -0.344
61 H15A H H15A N N N 0 0.498 -3.505 -0.827



TOK : Chemical Bonds

Total Number of Bonds: 66
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 H1 C H sing 1.09 N N
2 C1 H1A C H sing 1.09 N N
3 C2 C1 C C sing 1.53 N N
4 C2 H2 C H sing 1.09 N N
5 C2 H2A C H sing 1.09 N N
6 C3 C2 C C sing 1.53 N N
7 C3 H3 C H sing 1.09 N N
8 O3 C3 O C sing 1.43 N N
9 O3 HO3 O H sing 0.97 N N
10 C4 C3 C C sing 1.53 N N
11 C4 C5 C C sing 1.52 N N
12 C4 H4 C H sing 1.09 N N
13 C4 H4A C H sing 1.09 N N
14 C5 C10 C C sing 1.5 N N
15 C6 C5 C C doub 1.3 N N
16 C6 C7 C C sing 1.5 N N
17 C6 H6 C H sing 1.08 N N
18 C7 C8 C C sing 1.53 N N
19 C7 H7 C H sing 1.09 N N
20 C7 H7A C H sing 1.09 N N
21 C8 C14 C C sing 1.52 N N
22 C8 C9 C C sing 1.54 N N
23 C8 H8 C H sing 1.09 N N
24 C9 C11 C C sing 1.53 N N
25 C9 H9 C H sing 1.09 N N
26 C10 C1 C C sing 1.53 N N
27 C10 C9 C C sing 1.52 N N
28 C11 C12 C C sing 1.54 N N
29 C11 H11 C H sing 1.09 N N
30 C11 H11A C H sing 1.09 N N
31 C12 H12 C H sing 1.09 N N
32 C12 H12A C H sing 1.09 N N
33 C13 C12 C C sing 1.51 N N
34 C13 C17 C C sing 1.49 N N
35 C14 C13 C C sing 1.56 N N
36 C14 H14 C H sing 1.09 N N
37 C15 C14 C C sing 1.53 N N
38 C15 C16 C C sing 1.53 N N
39 C15 H15 C H sing 1.09 N N
40 C16 C17 C C doub 1.33 N N
41 C16 H16 C H sing 1.08 N N
42 C17 N48 C N sing 1.39 N N
43 C18 C13 C C sing 1.53 N N
44 C18 H18 C H sing 1.09 N N
45 C18 H18A C H sing 1.09 N N
46 C18 H18B C H sing 1.09 N N
47 C19 C10 C C sing 1.53 N N
48 C19 H19 C H sing 1.09 N N
49 C19 H19A C H sing 1.09 N N
50 C19 H19B C H sing 1.09 N N
51 N48 C52 N C sing 1.36 N Y
52 N48 C49 N C sing 1.38 N Y
53 C49 C53 C C sing 1.39 N Y
54 C49 C50 C C doub 1.41 N Y
55 C50 C56 C C sing 1.4 N Y
56 N51 C50 N C sing 1.36 N Y
57 C52 N51 C N doub 1.3 N Y
58 C52 H52 C H sing 1.08 N N
59 C53 C54 C C doub 1.38 N Y
60 C53 H53 C H sing 1.08 N N
61 C54 C55 C C sing 1.39 N Y
62 C54 H54 C H sing 1.08 N N
63 C55 H55 C H sing 1.08 N N
64 C56 C55 C C doub 1.37 N Y
65 C56 H56 C H sing 1.08 N N
66 C15 H15A C H sing 1.09 N N



TOK : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
TOK 3swz Open in New Window Bound ligand 4 1