Chemical Components in the PDB

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9KY : Summary

Code

9KY

One-letter code

X

Molecule name

(2S)-N,2-dicyclohexyl-2-{2-[4-(hydroxymethyl)phenyl]-1H-benzimidazol-1-yl}acetamide

Systematic names

ProgramVersionName
ACDLabs 12.01 (2S)-N,2-dicyclohexyl-2-{2-[4-(hydroxymethyl)phenyl]-1H-benzimidazol-1-yl}acetamide
OpenEye OEToolkits 2.0.6 (2~{S})-~{N},2-dicyclohexyl-2-[2-[4-(hydroxymethyl)phenyl]benzimidazol-1-yl]ethanamide

Formula

C28 H35 N3 O2

Formal charge

0

Molecular weight

445.596 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 n3c5c(n(C(C(NC1CCCCC1)=O)C2CCCCC2)c3c4ccc(cc4)CO)cccc5
SMILES CACTVS 3.385 OCc1ccc(cc1)c2nc3ccccc3n2[CH](C4CCCCC4)C(=O)NC5CCCCC5
SMILES OpenEye OEToolkits 2.0.6 c1ccc2c(c1)nc(n2C(C3CCCCC3)C(=O)NC4CCCCC4)c5ccc(cc5)CO
Canonical SMILES CACTVS 3.385 OCc1ccc(cc1)c2nc3ccccc3n2[C@@H](C4CCCCC4)C(=O)NC5CCCCC5
Canonical SMILES OpenEye OEToolkits 2.0.6 c1ccc2c(c1)nc(n2[C@@H](C3CCCCC3)C(=O)NC4CCCCC4)c5ccc(cc5)CO

IUPAC InChI

InChI=1S/C28H35N3O2/c32-19-20-15-17-22(18-16-20)27-30-24-13-7-8-14-25(24)31(27)26(21-9-3-1-4-10-21)28(33)29-23-11-5-2-6-12-23/h7-8,13-18,21,23,26,32H,1-6,9-12,19H2,(H,29,33)/t26-/m0/s1

IUPAC InChI key

VNQAIQZVCULCDE-SANMLTNESA-N
9KY

wwPDB Information

Atom count

68 (33 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-05-19

Last modified at

2017-06-30

Status

Released

Obsoleted

Not Assigned



9KY : Atoms of Molecule

Total Number of Atoms: 68
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N3 N N1 N Y N 0 -1.464 -2.994 0.998
2 C4 C C1 N N N 0 0.3 0.785 0.261
3 C5 C C2 S N N 0 -0.783 0.172 -0.589
4 C6 C C3 N Y N 0 -2.625 -1.152 0.553
5 C7 C C4 N Y N 0 -2.691 -2.433 1.13
6 C13 C C5 N Y N 0 1.413 -1.657 -0.899
7 C15 C C6 N Y N 0 2.772 -3.681 0.425
8 C17 C C7 N Y N 0 3.416 -2.919 -0.534
9 C21 C C8 N N N 0 4.862 -3.189 -0.86
10 C22 C C9 N N N 0 -1.295 2.484 -1.386
11 C24 C C10 N N N 0 1.383 3.552 1.417
12 C26 C C11 N Y N 0 -4.926 -0.796 1.105
13 C28 C C12 N N N 0 -4.032 1.658 -2.025
14 C1 C C13 N Y N 0 -0.661 -2.158 0.387
15 N2 N N2 N Y N 0 -1.333 -1.003 0.091
16 O10 O O1 N N N 0 0.482 0.385 1.392
17 N8 N N3 N N N 0 1.067 1.776 -0.235
18 C14 C C14 N N N 0 2.058 2.433 0.621
19 C31 C C15 N N N 0 2.418 4.239 2.31
20 C32 C C16 N N N 0 3.53 4.83 1.441
21 C30 C C17 N N N 0 4.205 3.711 0.646
22 C25 C C18 N N N 0 3.17 3.024 -0.248
23 C11 C C19 N N N 0 -1.895 1.198 -0.814
24 C29 C C20 N N N 0 -2.408 3.51 -1.611
25 C33 C C21 N N N 0 -3.432 2.944 -2.596
26 C23 C C22 N N N 0 -2.92 0.632 -1.8
27 C19 C C23 N Y N 0 -3.894 -2.873 1.691
28 C27 C C24 N Y N 0 -4.991 -2.06 1.674
29 C18 C C25 N Y N 0 -3.751 -0.34 0.547
30 C9 C C26 N Y N 0 0.758 -2.423 0.067
31 C12 C C27 N Y N 0 1.448 -3.439 0.729
32 C16 C C28 N Y N 0 2.737 -1.91 -1.194
33 O20 O O2 N N N 0 4.94 -4.15 -1.915
34 H1 H H1 N N N 0 -0.365 -0.127 -1.55
35 H2 H H2 N N N 0 0.883 -0.872 -1.418
36 H3 H H3 N N N 0 3.307 -4.468 0.936
37 H4 H H4 N N N 0 5.342 -2.263 -1.176
38 H5 H H5 N N N 0 5.368 -3.577 0.023
39 H6 H H6 N N N 0 -0.566 2.888 -0.683
40 H7 H H7 N N N 0 -0.805 2.266 -2.334
41 H8 H H8 N N N 0 0.956 4.281 0.728
42 H9 H H9 N N N 0 0.591 3.131 2.036
43 H10 H H10 N N N 0 -5.803 -0.165 1.1
44 H11 H H11 N N N 0 -4.523 1.876 -1.076
45 H12 H H12 N N N 0 -4.762 1.254 -2.727
46 H13 H H13 N N N 0 0.963 2.054 -1.158
47 H14 H H14 N N N 0 2.484 1.704 1.31
48 H15 H H15 N N N 0 1.937 5.036 2.877
49 H16 H H16 N N N 0 2.844 3.509 2.999
50 H17 H H17 N N N 0 3.103 5.559 0.753
51 H18 H H18 N N N 0 4.267 5.319 2.078
52 H19 H H19 N N N 0 4.997 4.132 0.027
53 H20 H H20 N N N 0 4.631 2.982 1.335
54 H21 H H21 N N N 0 3.651 2.227 -0.814
55 H22 H H22 N N N 0 2.744 3.754 -0.937
56 H23 H H23 N N N 0 -2.386 1.416 0.134
57 H24 H H24 N N N 0 -2.898 3.728 -0.662
58 H25 H H25 N N N 0 -1.98 4.427 -2.018
59 H26 H H26 N N N 0 -2.941 2.726 -3.545
60 H27 H H27 N N N 0 -4.225 3.675 -2.757
61 H28 H H28 N N N 0 -3.347 -0.284 -1.393
62 H29 H H29 N N N 0 -2.429 0.414 -2.749
63 H30 H H30 N N N 0 -3.955 -3.855 2.137
64 H31 H H31 N N N 0 -5.918 -2.404 2.109
65 H32 H H32 N N N 0 -3.707 0.645 0.105
66 H33 H H33 N N N 0 0.947 -4.035 1.477
67 H34 H H34 N N N 0 3.245 -1.318 -1.941
68 H35 H H35 N N N 0 5.844 -4.372 -2.178



9KY : Chemical Bonds

Total Number of Bonds: 72
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C33 C28 C C sing 1.53 N N
2 C33 C29 C C sing 1.53 N N
3 C28 C23 C C sing 1.53 N N
4 C29 C22 C C sing 1.53 N N
5 C23 C11 C C sing 1.53 N N
6 C22 C11 C C sing 1.53 N N
7 C11 C5 C C sing 1.53 N N
8 O10 C4 O C doub 1.21 N N
9 C5 C4 C C sing 1.51 N N
10 C5 N2 C N sing 1.46 N N
11 C4 N8 C N sing 1.35 N N
12 C18 C26 C C doub 1.38 N Y
13 C18 C6 C C sing 1.39 N Y
14 C26 C27 C C sing 1.39 N Y
15 N2 C6 N C sing 1.38 N Y
16 N2 C1 N C sing 1.37 N Y
17 C6 C7 C C doub 1.41 N Y
18 C13 C16 C C doub 1.38 N Y
19 C13 C9 C C sing 1.4 N Y
20 C16 C17 C C sing 1.38 N Y
21 O20 C21 O C sing 1.43 N N
22 N8 C14 N C sing 1.47 N N
23 C1 C9 C C sing 1.48 N N
24 C1 N3 C N doub 1.31 N Y
25 C27 C19 C C doub 1.37 N Y
26 C9 C12 C C doub 1.4 N Y
27 C7 C19 C C sing 1.4 N Y
28 C7 N3 C N sing 1.36 N Y
29 C14 C25 C C sing 1.53 N N
30 C14 C24 C C sing 1.53 N N
31 C17 C21 C C sing 1.51 N N
32 C17 C15 C C doub 1.38 N Y
33 C25 C30 C C sing 1.53 N N
34 C12 C15 C C sing 1.38 N Y
35 C24 C31 C C sing 1.53 N N
36 C30 C32 C C sing 1.53 N N
37 C31 C32 C C sing 1.53 N N
38 C5 H1 C H sing 1.09 N N
39 C13 H2 C H sing 1.08 N N
40 C15 H3 C H sing 1.08 N N
41 C21 H4 C H sing 1.09 N N
42 C21 H5 C H sing 1.09 N N
43 C22 H6 C H sing 1.09 N N
44 C22 H7 C H sing 1.09 N N
45 C24 H8 C H sing 1.09 N N
46 C24 H9 C H sing 1.09 N N
47 C26 H10 C H sing 1.08 N N
48 C28 H11 C H sing 1.09 N N
49 C28 H12 C H sing 1.09 N N
50 N8 H13 N H sing 0.97 N N
51 C14 H14 C H sing 1.09 N N
52 C31 H15 C H sing 1.09 N N
53 C31 H16 C H sing 1.09 N N
54 C32 H17 C H sing 1.09 N N
55 C32 H18 C H sing 1.09 N N
56 C30 H19 C H sing 1.09 N N
57 C30 H20 C H sing 1.09 N N
58 C25 H21 C H sing 1.09 N N
59 C25 H22 C H sing 1.09 N N
60 C11 H23 C H sing 1.09 N N
61 C29 H24 C H sing 1.09 N N
62 C29 H25 C H sing 1.09 N N
63 C33 H26 C H sing 1.09 N N
64 C33 H27 C H sing 1.09 N N
65 C23 H28 C H sing 1.09 N N
66 C23 H29 C H sing 1.09 N N
67 C19 H30 C H sing 1.08 N N
68 C27 H31 C H sing 1.08 N N
69 C18 H32 C H sing 1.08 N N
70 C12 H33 C H sing 1.08 N N
71 C16 H34 C H sing 1.08 N N
72 O20 H35 O H sing 0.97 N N



9KY : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
9KY 5q0l Open in New Window Bound ligand 2 1