Chemical Components in the PDB

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YOD : Summary

Code

YOD

One-letter code

X

Molecule name

(1R,3S,5S,7S)-N-[(1r,4R)-4-aminocyclohexyl]-3-[(methylsulfanyl)methyl]-5-phenyladamantane-1-carboxamide

Systematic names

ProgramVersionName
ACDLabs 12.01 (1R,3S,5S,7S)-N-[(1r,4R)-4-aminocyclohexyl]-3-[(methylsulfanyl)methyl]-5-phenyladamantane-1-carboxamide
OpenEye OEToolkits 2.0.7 (1~{R},3~{S},5~{S},7~{S})-~{N}-(4-azanylcyclohexyl)-3-(methylsulfanylmethyl)-5-phenyl-adamantane-1-carboxamide

Formula

C25 H36 N2 O S

Formal charge

0

Molecular weight

412.631 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(NC1CCC(N)CC1)C12CC3CC(CC(CSC)(C3)C1)(C2)c1ccccc1
SMILES CACTVS 3.385 CSC[C]12C[CH]3C[C](C1)(C[C](C3)(C2)c4ccccc4)C(=O)N[CH]5CC[CH](N)CC5
SMILES OpenEye OEToolkits 2.0.7 CSCC12CC3CC(C1)(CC(C3)(C2)C(=O)NC4CCC(CC4)N)c5ccccc5
Canonical SMILES CACTVS 3.385 CSC[C@]12C[C@@H]3C[C@](C1)(C[C@@](C3)(C2)c4ccccc4)C(=O)N[C@H]5CC[C@H](N)CC5
Canonical SMILES OpenEye OEToolkits 2.0.7 CSC[C@@]12C[C@H]3C[C@@](C1)(C[C@](C3)(C2)C(=O)NC4CCC(CC4)N)c5ccccc5

IUPAC InChI

InChI=1S/C25H36N2OS/c1-29-17-23-11-18-12-24(14-23,19-5-3-2-4-6-19)16-25(13-18,15-23)22(28)27-21-9-7-20(26)8-10-21/h2-6,18,20-21H,7-17,26H2,1H3,(H,27,28)/t18-,20-,21-,23-,24+,25-/m0/s1

IUPAC InChI key

DETLZYCOWYAPEH-ONOIFOFISA-N
YOD

wwPDB Information

Atom count

65 (29 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-03-17

Last modified at

2021-11-19

Status

Released

Obsoleted

Not Assigned



YOD : Atoms of Molecule

Total Number of Atoms: 65
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C21 C C1 N N N 0 3.689 0.515 0.183
2 C22 C C2 N N N 0 4.618 0.059 1.311
3 C23 C C3 N N N 0 6.065 0.397 0.947
4 C24 C C4 N N N 0 6.446 -0.322 -0.35
5 C26 C C5 N N N 0 5.517 0.134 -1.477
6 C27 C C6 N N N 0 4.07 -0.203 -1.113
7 C11 C C7 N Y N 0 -2.185 -2.637 -0.084
8 C13 C C8 N Y N 0 -3.474 -4.209 -1.349
9 C14 C C9 N Y N 0 -2.741 -5.247 -0.804
10 C29 C C10 N N N 0 -1.081 1.514 -0.389
11 C15 C C11 N Y N 0 -1.728 -4.98 0.096
12 C10 C C12 N N N 0 -2.083 -1.054 1.822
13 C12 C C13 N Y N 0 -3.196 -2.904 -0.989
14 C01 C C14 N N N 0 -4.317 4.79 -1.254
15 C03 C C15 N N N 0 -3.475 2.123 -0.766
16 C04 C C16 S N N 0 -2.528 1.177 -0.025
17 C05 C C17 N N N 0 -2.725 1.337 1.484
18 C06 C C18 S N N 0 -1.779 0.391 2.225
19 C07 C C19 N N N 0 -0.332 0.728 1.861
20 C08 C C20 N N N 0 -2.832 -0.268 -0.428
21 C09 C C21 S N N 0 -1.886 -1.214 0.313
22 C16 C C22 N Y N 0 -1.453 -3.675 0.461
23 C17 C C23 N N N 0 -0.439 -0.877 -0.051
24 C18 C C24 R N N 0 -0.135 0.568 0.353
25 C19 C C25 N N N 0 1.291 0.9 -0.006
26 N20 N N1 N N N 0 2.303 0.192 0.532
27 N25 N N2 N N N 0 7.836 0.002 -0.699
28 O28 O O1 N N N 0 1.527 1.805 -0.778
29 S02 S S1 N N N 0 -3.114 3.835 -0.288
30 H1 H H1 N N N 0 3.787 1.592 0.045
31 H2 H H2 N N N 0 4.347 0.571 2.234
32 H3 H H3 N N N 0 4.52 -1.017 1.449
33 H4 H H4 N N N 0 6.164 1.473 0.808
34 H5 H H5 N N N 0 6.727 0.072 1.75
35 H6 H H6 N N N 0 6.348 -1.398 -0.211
36 H7 H H7 N N N 0 5.615 1.211 -1.616
37 H8 H H8 N N N 0 5.788 -0.378 -2.4
38 H9 H H9 N N N 0 3.972 -1.28 -0.974
39 H10 H H10 N N N 0 3.408 0.121 -1.916
40 H11 H H11 N N N 0 -4.266 -4.418 -2.053
41 H12 H H12 N N N 0 -2.959 -6.267 -1.086
42 H13 H H13 N N N 0 -0.941 1.4 -1.464
43 H14 H H14 N N N 0 -0.865 2.543 -0.101
44 H15 H H15 N N N 0 -1.155 -5.791 0.522
45 H16 H H16 N N N 0 -1.409 -1.728 2.35
46 H17 H H17 N N N 0 -3.114 -1.294 2.081
47 H18 H H18 N N N 0 -3.768 -2.092 -1.414
48 H19 H H19 N N N 0 -4.155 4.609 -2.316
49 H20 H H20 N N N 0 -5.327 4.483 -0.982
50 H21 H H21 N N N 0 -4.191 5.852 -1.043
51 H22 H H22 N N N 0 -3.334 2.009 -1.841
52 H23 H H23 N N N 0 -4.506 1.883 -0.507
53 H24 H H24 N N N 0 -2.509 2.366 1.771
54 H25 H H25 N N N 0 -3.757 1.097 1.743
55 H26 H H26 N N N 0 -1.92 0.505 3.3
56 H27 H H27 N N N 0 -0.115 1.757 2.149
57 H28 H H28 N N N 0 0.342 0.054 2.39
58 H29 H H29 N N N 0 -3.863 -0.508 -0.169
59 H30 H H30 N N N 0 -2.692 -0.382 -1.503
60 H31 H H31 N N N 0 -0.666 -3.467 1.171
61 H32 H H32 N N N 0 0.235 -1.551 0.478
62 H33 H H33 N N N 0 -0.298 -0.991 -1.125
63 H34 H H34 N N N 0 2.115 -0.532 1.15
64 H35 H H35 N N N 0 8.111 -0.46 -1.552
65 H36 H H36 N N N 0 7.967 1.0 -0.77



YOD : Chemical Bonds

Total Number of Bonds: 69
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C13 C14 C C doub 1.38 N Y
2 C13 C12 C C sing 1.38 N Y
3 C14 C15 C C sing 1.38 N Y
4 C12 C11 C C doub 1.38 N Y
5 C15 C16 C C doub 1.38 N Y
6 C11 C16 C C sing 1.38 N Y
7 C11 C09 C C sing 1.51 N N
8 O28 C19 O C doub 1.21 N N
9 C17 C09 C C sing 1.53 N N
10 C17 C18 C C sing 1.53 N N
11 C09 C10 C C sing 1.53 N N
12 C09 C08 C C sing 1.53 N N
13 C10 C06 C C sing 1.53 N N
14 C26 C27 C C sing 1.53 N N
15 C26 C24 C C sing 1.53 N N
16 C19 C18 C C sing 1.51 N N
17 C19 N20 C N sing 1.35 N N
18 C27 C21 C C sing 1.53 N N
19 C21 N20 C N sing 1.47 N N
20 C21 C22 C C sing 1.53 N N
21 C18 C07 C C sing 1.53 N N
22 C18 C29 C C sing 1.53 N N
23 C07 C06 C C sing 1.53 N N
24 N25 C24 N C sing 1.47 N N
25 C06 C05 C C sing 1.53 N N
26 C08 C04 C C sing 1.53 N N
27 C24 C23 C C sing 1.53 N N
28 C23 C22 C C sing 1.53 N N
29 C29 C04 C C sing 1.53 N N
30 C04 C05 C C sing 1.53 N N
31 C04 C03 C C sing 1.53 N N
32 C03 S02 C S sing 1.81 N N
33 S02 C01 S C sing 1.81 N N
34 C21 H1 C H sing 1.09 N N
35 C22 H2 C H sing 1.09 N N
36 C22 H3 C H sing 1.09 N N
37 C23 H4 C H sing 1.09 N N
38 C23 H5 C H sing 1.09 N N
39 C24 H6 C H sing 1.09 N N
40 C26 H7 C H sing 1.09 N N
41 C26 H8 C H sing 1.09 N N
42 C27 H9 C H sing 1.09 N N
43 C27 H10 C H sing 1.09 N N
44 C13 H11 C H sing 1.08 N N
45 C14 H12 C H sing 1.08 N N
46 C29 H13 C H sing 1.09 N N
47 C29 H14 C H sing 1.09 N N
48 C15 H15 C H sing 1.08 N N
49 C10 H16 C H sing 1.09 N N
50 C10 H17 C H sing 1.09 N N
51 C12 H18 C H sing 1.08 N N
52 C01 H19 C H sing 1.09 N N
53 C01 H20 C H sing 1.09 N N
54 C01 H21 C H sing 1.09 N N
55 C03 H22 C H sing 1.09 N N
56 C03 H23 C H sing 1.09 N N
57 C05 H24 C H sing 1.09 N N
58 C05 H25 C H sing 1.09 N N
59 C06 H26 C H sing 1.09 N N
60 C07 H27 C H sing 1.09 N N
61 C07 H28 C H sing 1.09 N N
62 C08 H29 C H sing 1.09 N N
63 C08 H30 C H sing 1.09 N N
64 C16 H31 C H sing 1.08 N N
65 C17 H32 C H sing 1.09 N N
66 C17 H33 C H sing 1.09 N N
67 N20 H34 N H sing 0.97 N N
68 N25 H35 N H sing 1.01 N N
69 N25 H36 N H sing 1.01 N N



YOD : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
YOD 7lyd Open in New Window Bound ligand 1 1