Chemical Components in the PDB

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1II : Summary

Code

1II

One-letter code

X

Molecule name

3-[1-[4,4-bis(4-fluorophenyl)butyl]piperidin-4-yl]-1~{H}-benzimidazol-2-one

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 3-[1-[4,4-bis(4-fluorophenyl)butyl]piperidin-4-yl]-1~{H}-benzimidazol-2-one

Formula

C28 H29 F2 N3 O

Formal charge

0

Molecular weight

461.546 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 Fc1ccc(cc1)C(CCCN2CCC(CC2)N3C(=O)Nc4ccccc34)c5ccc(F)cc5
SMILES OpenEye OEToolkits 2.0.7 c1ccc2c(c1)NC(=O)N2C3CCN(CC3)CCCC(c4ccc(cc4)F)c5ccc(cc5)F
Canonical SMILES CACTVS 3.385 Fc1ccc(cc1)C(CCCN2CCC(CC2)N3C(=O)Nc4ccccc34)c5ccc(F)cc5
Canonical SMILES OpenEye OEToolkits 2.0.7 c1ccc2c(c1)NC(=O)N2C3CCN(CC3)CCCC(c4ccc(cc4)F)c5ccc(cc5)F

IUPAC InChI

InChI=1S/C28H29F2N3O/c29-22-11-7-20(8-12-22)25(21-9-13-23(30)14-10-21)4-3-17-32-18-15-24(16-19-32)33-27-6-2-1-5-26(27)31-28(33)34/h1-2,5-14,24-25H,3-4,15-19H2,(H,31,34)

IUPAC InChI key

YVUQSNJEYSNKRX-UHFFFAOYSA-N
1II

wwPDB Information

Atom count

63 (34 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2022-01-23

Last modified at

2022-04-29

Status

Released

Obsoleted

Not Assigned



1II : Atoms of Molecule

Total Number of Atoms: 63
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C07 C C1 N N N 0 3.94 -0.707 -0.308
2 C08 C C2 N N N 0 2.931 -0.357 0.789
3 C09 C C3 N N N 0 3.379 -0.273 -1.665
4 C10 C C4 N N N 0 1.596 -1.041 0.485
5 C11 C C5 N N N 0 2.031 -0.959 -1.898
6 C12 C C6 N N N 0 -0.244 -1.12 -1.086
7 C13 C C7 N N N 0 -1.234 -0.516 -0.089
8 C14 C C8 N Y N 0 6.441 -0.612 0.154
9 C15 C C9 N N N 0 -2.635 -1.067 -0.363
10 C16 C C10 N N N 0 5.364 1.326 0.018
11 C17 C C11 N N N 0 -3.625 -0.462 0.635
12 C18 C C12 N Y N 0 7.363 0.417 0.357
13 C19 C C13 N Y N 0 6.862 -1.932 0.185
14 C20 C C14 N Y N 0 -3.728 1.023 0.403
15 C21 C C15 N Y N 0 -4.979 -1.096 0.444
16 C22 C C16 N Y N 0 8.696 0.115 0.587
17 C23 C C17 N Y N 0 8.193 -2.224 0.415
18 C24 C C18 N Y N 0 9.107 -1.204 0.615
19 C25 C C19 N Y N 0 -3.996 1.508 -0.864
20 C26 C C20 N Y N 0 -5.648 -1.635 1.528
21 C27 C C21 N Y N 0 -3.56 1.9 1.458
22 C28 C C22 N Y N 0 -5.554 -1.132 -0.812
23 C29 C C23 N Y N 0 -4.09 2.87 -1.077
24 C30 C C24 N Y N 0 -6.889 -2.216 1.355
25 C31 C C25 N Y N 0 -3.655 3.263 1.247
26 C32 C C26 N Y N 0 -6.799 -1.708 -0.987
27 C33 C C27 N Y N 0 -3.917 3.749 -0.022
28 C34 C C28 N Y N 0 -7.464 -2.258 0.096
29 F01 F F1 N N N 0 -4.009 5.081 -0.23
30 F02 F F2 N N N 0 -8.68 -2.821 -0.074
31 N04 N N1 N N N 0 1.101 -0.591 -0.823
32 N05 N N2 N N N 0 5.203 -0.009 -0.054
33 N06 N N3 N N N 0 6.655 1.614 0.27
34 O03 O O1 N N N 0 4.476 2.147 -0.117
35 H1 H H1 N N N 0 4.114 -1.783 -0.313
36 H2 H H2 N N N 0 3.306 -0.702 1.752
37 H3 H H3 N N N 0 2.789 0.724 0.82
38 H4 H H4 N N N 0 3.243 0.809 -1.673
39 H5 H H5 N N N 0 4.075 -0.558 -2.455
40 H6 H H6 N N N 0 1.738 -2.121 0.468
41 H7 H H7 N N N 0 0.872 -0.781 1.256
42 H8 H H8 N N N 0 1.622 -0.64 -2.857
43 H9 H H9 N N N 0 2.171 -2.04 -1.904
44 H10 H H10 N N N 0 -0.235 -2.205 -0.978
45 H11 H H11 N N N 0 -0.545 -0.858 -2.101
46 H12 H H12 N N N 0 -0.933 -0.778 0.926
47 H13 H H13 N N N 0 -1.242 0.569 -0.197
48 H14 H H14 N N N 0 -2.936 -0.805 -1.378
49 H15 H H15 N N N 0 -2.626 -2.151 -0.255
50 H16 H H16 N N N 0 -3.276 -0.648 1.65
51 H17 H H17 N N N 0 6.152 -2.731 0.029
52 H18 H H18 N N N 0 9.411 0.908 0.743
53 H19 H H19 N N N 0 8.522 -3.253 0.439
54 H20 H H20 N N N 0 10.145 -1.439 0.794
55 H21 H H21 N N N 0 -4.131 0.822 -1.687
56 H22 H H22 N N N 0 -5.199 -1.602 2.51
57 H23 H H23 N N N 0 -3.355 1.52 2.448
58 H24 H H24 N N N 0 -5.031 -0.711 -1.658
59 H25 H H25 N N N 0 -4.299 3.248 -2.067
60 H26 H H26 N N N 0 -7.411 -2.638 2.201
61 H27 H H27 N N N 0 -3.523 3.947 2.072
62 H28 H H28 N N N 0 -7.246 -1.74 -1.969
63 H30 H H30 N N N 0 7.029 2.503 0.368



1II : Chemical Bonds

Total Number of Bonds: 67
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 F01 C33 F C sing 1.35 N N
2 F02 C34 F C sing 1.35 N N
3 C33 C29 C C doub 1.38 N Y
4 C33 C31 C C sing 1.38 N Y
5 C32 C34 C C doub 1.38 N Y
6 C32 C28 C C sing 1.38 N Y
7 C29 C25 C C sing 1.38 N Y
8 C34 C30 C C sing 1.38 N Y
9 C31 C27 C C doub 1.38 N Y
10 C28 C21 C C doub 1.38 N Y
11 C30 C26 C C doub 1.38 N Y
12 C25 C20 C C doub 1.38 N Y
13 C27 C20 C C sing 1.38 N Y
14 C20 C17 C C sing 1.51 N N
15 C21 C26 C C sing 1.38 N Y
16 C21 C17 C C sing 1.51 N N
17 C17 C15 C C sing 1.53 N N
18 C15 C13 C C sing 1.53 N N
19 C12 C13 C C sing 1.53 N N
20 C12 N04 C N sing 1.47 N N
21 C11 N04 C N sing 1.47 N N
22 C11 C09 C C sing 1.53 N N
23 N04 C10 N C sing 1.47 N N
24 C09 C07 C C sing 1.53 N N
25 C10 C08 C C sing 1.53 N N
26 C07 C08 C C sing 1.53 N N
27 C07 N05 C N sing 1.47 N N
28 N05 C14 N C sing 1.39 N N
29 N05 C16 N C sing 1.35 N N
30 C19 C14 C C doub 1.39 N Y
31 C19 C23 C C sing 1.38 N Y
32 O03 C16 O C doub 1.22 N N
33 C14 C18 C C sing 1.4 N Y
34 C16 N06 C N sing 1.35 N N
35 C23 C24 C C doub 1.38 N Y
36 C18 N06 C N sing 1.39 N N
37 C18 C22 C C doub 1.39 N Y
38 C24 C22 C C sing 1.38 N Y
39 C07 H1 C H sing 1.09 N N
40 C08 H2 C H sing 1.09 N N
41 C08 H3 C H sing 1.09 N N
42 C09 H4 C H sing 1.09 N N
43 C09 H5 C H sing 1.09 N N
44 C10 H6 C H sing 1.09 N N
45 C10 H7 C H sing 1.09 N N
46 C11 H8 C H sing 1.09 N N
47 C11 H9 C H sing 1.09 N N
48 C12 H10 C H sing 1.09 N N
49 C12 H11 C H sing 1.09 N N
50 C13 H12 C H sing 1.09 N N
51 C13 H13 C H sing 1.09 N N
52 C15 H14 C H sing 1.09 N N
53 C15 H15 C H sing 1.09 N N
54 C17 H16 C H sing 1.09 N N
55 C19 H17 C H sing 1.08 N N
56 C22 H18 C H sing 1.08 N N
57 C23 H19 C H sing 1.08 N N
58 C24 H20 C H sing 1.08 N N
59 C25 H21 C H sing 1.08 N N
60 C26 H22 C H sing 1.08 N N
61 C27 H23 C H sing 1.08 N N
62 C28 H24 C H sing 1.08 N N
63 C29 H25 C H sing 1.08 N N
64 C30 H26 C H sing 1.08 N N
65 C31 H27 C H sing 1.08 N N
66 C32 H28 C H sing 1.08 N N
67 N06 H30 N H sing 0.97 N N



1II : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
1II 7wll Open in New Window Bound ligand 1 1
1II 8gu1 Open in New Window Bound ligand 2 1