Chemical Components in the PDB

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M9B : Summary

Code

M9B

One-letter code

X

Molecule name

1-alpha-hydroxy-vitamin D3

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 (1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-7~{a}-methyl-1-[(2~{R})-6-methylheptan-2-yl]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol

Formula

C27 H44 O2

Formal charge

0

Molecular weight

400.637 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CC(C)CCC[CH](C)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C[CH](O)C3=C
SMILES OpenEye OEToolkits 2.0.7 CC(C)CCCC(C)C1CCC2C1(CCCC2=CC=C3CC(CC(C3=C)O)O)C
Canonical SMILES CACTVS 3.385 CC(C)CCC[C@@H](C)[C@H]1CC[C@H]2/C(CCC[C@]12C)=C/C=C3/C[C@@H](O)C[C@H](O)C3=C
Canonical SMILES OpenEye OEToolkits 2.0.7 C[C@H](CCCC(C)C)[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

IUPAC InChI

InChI=1S/C27H44O2/c1-18(2)8-6-9-19(3)24-13-14-25-21(10-7-15-27(24,25)5)11-12-22-16-23(28)17-26(29)20(22)4/h11-12,18-19,23-26,28-29H,4,6-10,13-17H2,1-3,5H3/b21-11+,22-12-/t19-,23-,24-,25+,26+,27-/m1/s1

IUPAC InChI key

OFHCOWSQAMBJIW-AVJTYSNKSA-N
M9B

wwPDB Information

Atom count

73 (29 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-10-08

Last modified at

2020-10-09

Status

Released

Obsoleted

Not Assigned



M9B : Atoms of Molecule

Total Number of Atoms: 73
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C1 N N N 0 5.799 0.111 -0.482
2 C14 C C2 S N N 0 -0.043 1.808 1.174
3 C5 C C3 N N N 0 4.446 0.045 0.198
4 C6 C C4 N N N 0 4.195 -1.12 1.07
5 C11 C C5 N N N 0 0.384 3.247 -1.365
6 C7 C C6 N N N 0 3.516 1.005 0.015
7 C8 C C7 N N N 0 2.22 0.907 0.69
8 C9 C C8 N N N 0 1.301 1.855 0.51
9 C10 C C9 N N N 0 1.54 3.063 -0.384
10 C12 C C10 N N N 0 -0.972 3.178 -0.665
11 C13 C C11 R N N 0 -1.081 1.834 0.016
12 C3 C C12 R N N 0 6.102 -1.263 -1.089
13 O O O1 N N N 0 7.397 -1.241 -1.692
14 C1 C C13 S N N 0 4.643 -2.472 0.55
15 C15 C C14 N N N 0 -0.41 0.507 1.892
16 C16 C C15 N N N 0 -1.964 0.552 1.91
17 C17 C C16 R N N 0 -2.389 1.477 0.704
18 C18 C C17 N N N 0 -0.733 0.73 -0.985
19 C19 C C18 N N N 0 3.604 -0.99 2.258
20 C2 C C19 N N N 0 6.068 -2.331 0.0050
21 C20 C C20 R N N 0 -3.308 0.724 -0.261
22 C21 C C21 N N N 0 -3.726 1.656 -1.4
23 C22 C C22 N N N 0 -4.553 0.246 0.489
24 C23 C C23 N N N 0 -5.412 -0.612 -0.442
25 C24 C C24 N N N 0 -6.657 -1.089 0.308
26 C25 C C25 N N N 0 -7.516 -1.948 -0.623
27 C26 C C26 N N N 0 -6.752 -3.221 -0.992
28 C27 C C27 N N N 0 -8.819 -2.322 0.085
29 O1 O O2 N N N 0 3.767 -2.899 -0.495
30 H1 H H1 N N N 0 5.778 0.864 -1.27
31 H2 H H2 N N N 0 6.566 0.367 0.249
32 H3 H H3 N N N 0 -0.176 2.664 1.835
33 H4 H H4 N N N 0 0.481 4.215 -1.857
34 H5 H H5 N N N 0 0.435 2.461 -2.118
35 H6 H H6 N N N 0 3.727 1.847 -0.628
36 H7 H H7 N N N 0 2.009 0.065 1.334
37 H8 H H8 N N N 0 2.465 2.918 -0.943
38 H9 H H9 N N N 0 1.632 3.956 0.235
39 H10 H H10 N N N 0 -1.043 3.968 0.083
40 H11 H H11 N N N 0 -1.772 3.289 -1.397
41 H12 H H12 N N N 0 5.353 -1.498 -1.846
42 H13 H H13 N N N 0 7.49 -0.59 -2.401
43 H14 H H14 N N N 0 4.63 -3.2 1.36
44 H15 H H15 N N N 0 -0.055 -0.36 1.334
45 H16 H H16 N N N 0 -0.012 0.505 2.906
46 H17 H H17 N N N 0 -2.369 -0.451 1.771
47 H18 H H18 N N N 0 -2.316 0.97 2.853
48 H19 H H19 N N N 0 -2.882 2.377 1.072
49 H20 H H20 N N N 0 0.317 0.812 -1.266
50 H21 H H21 N N N 0 -0.912 -0.243 -0.529
51 H22 H H22 N N N 0 -1.356 0.836 -1.873
52 H23 H H23 N N N 0 3.296 -0.014 2.603
53 H24 H H24 N N N 0 3.434 -1.86 2.875
54 H25 H H25 N N N 0 6.393 -3.285 -0.41
55 H26 H H26 N N N 0 6.739 -2.042 0.814
56 H27 H H27 N N N 0 -2.779 -0.136 -0.671
57 H28 H H28 N N N 0 -2.846 1.944 -1.975
58 H29 H H29 N N N 0 -4.433 1.142 -2.05
59 H30 H H30 N N N 0 -4.196 2.548 -0.986
60 H31 H H31 N N N 0 -4.252 -0.345 1.354
61 H32 H H32 N N N 0 -5.13 1.109 0.823
62 H33 H H33 N N N 0 -5.713 -0.02 -1.306
63 H34 H H34 N N N 0 -4.835 -1.474 -0.775
64 H35 H H35 N N N 0 -6.356 -1.681 1.173
65 H36 H H36 N N N 0 -7.234 -0.227 0.642
66 H37 H H37 N N N 0 -7.743 -1.385 -1.529
67 H38 H H38 N N N 0 -5.823 -2.954 -1.497
68 H39 H H39 N N N 0 -6.524 -3.783 -0.086
69 H40 H H40 N N N 0 -7.363 -3.832 -1.656
70 H41 H H41 N N N 0 -9.363 -1.415 0.348
71 H42 H H42 N N N 0 -9.431 -2.933 -0.578
72 H43 H H43 N N N 0 -8.592 -2.884 0.991
73 H44 H H44 N N N 0 2.845 -2.993 -0.222



M9B : Chemical Bonds

Total Number of Bonds: 75
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O1 C1 O C sing 1.43 N N
2 C2 C1 C C sing 1.53 N N
3 C2 C3 C C sing 1.53 N N
4 C26 C25 C C sing 1.53 N N
5 C1 C6 C C sing 1.52 N N
6 C27 C25 C C sing 1.53 N N
7 C19 C6 C C doub 1.33 N N
8 C25 C24 C C sing 1.53 N N
9 C6 C5 C C sing 1.48 N N
10 C3 C4 C C sing 1.53 N N
11 C3 O C O sing 1.43 N N
12 C4 C5 C C sing 1.52 N N
13 C24 C23 C C sing 1.53 N N
14 C5 C7 C C doub 1.35 Z N
15 C23 C22 C C sing 1.53 N N
16 C18 C13 C C sing 1.53 N N
17 C7 C8 C C sing 1.46 N N
18 C8 C9 C C doub 1.33 E N
19 C22 C20 C C sing 1.53 N N
20 C20 C17 C C sing 1.53 N N
21 C20 C21 C C sing 1.53 N N
22 C13 C12 C C sing 1.51 N N
23 C13 C14 C C sing 1.56 N N
24 C13 C17 C C sing 1.52 N N
25 C9 C14 C C sing 1.5 N N
26 C9 C10 C C sing 1.52 N N
27 C11 C12 C C sing 1.53 N N
28 C11 C10 C C sing 1.53 N N
29 C15 C16 C C sing 1.55 N N
30 C15 C14 C C sing 1.53 N N
31 C16 C17 C C sing 1.58 N N
32 C4 H1 C H sing 1.09 N N
33 C4 H2 C H sing 1.09 N N
34 C14 H3 C H sing 1.09 N N
35 C11 H4 C H sing 1.09 N N
36 C11 H5 C H sing 1.09 N N
37 C7 H6 C H sing 1.08 N N
38 C8 H7 C H sing 1.08 N N
39 C10 H8 C H sing 1.09 N N
40 C10 H9 C H sing 1.09 N N
41 C12 H10 C H sing 1.09 N N
42 C12 H11 C H sing 1.09 N N
43 C3 H12 C H sing 1.09 N N
44 O H13 O H sing 0.97 N N
45 C1 H14 C H sing 1.09 N N
46 C15 H15 C H sing 1.09 N N
47 C15 H16 C H sing 1.09 N N
48 C16 H17 C H sing 1.09 N N
49 C16 H18 C H sing 1.09 N N
50 C17 H19 C H sing 1.09 N N
51 C18 H20 C H sing 1.09 N N
52 C18 H21 C H sing 1.09 N N
53 C18 H22 C H sing 1.09 N N
54 C19 H23 C H sing 1.08 N N
55 C19 H24 C H sing 1.08 N N
56 C2 H25 C H sing 1.09 N N
57 C2 H26 C H sing 1.09 N N
58 C20 H27 C H sing 1.09 N N
59 C21 H28 C H sing 1.09 N N
60 C21 H29 C H sing 1.09 N N
61 C21 H30 C H sing 1.09 N N
62 C22 H31 C H sing 1.09 N N
63 C22 H32 C H sing 1.09 N N
64 C23 H33 C H sing 1.09 N N
65 C23 H34 C H sing 1.09 N N
66 C24 H35 C H sing 1.09 N N
67 C24 H36 C H sing 1.09 N N
68 C25 H37 C H sing 1.09 N N
69 C26 H38 C H sing 1.09 N N
70 C26 H39 C H sing 1.09 N N
71 C26 H40 C H sing 1.09 N N
72 C27 H41 C H sing 1.09 N N
73 C27 H42 C H sing 1.09 N N
74 C27 H43 C H sing 1.09 N N
75 O1 H44 O H sing 0.97 N N



M9B : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
M9B 6t0h Open in New Window Bound ligand 1 1