Chemical Components in the PDB

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5YS : Summary

Code

5YS

One-letter code

X

Molecule name

~{N}-[(1~{R})-1-(3-methoxyphenyl)ethyl]-4-pyridin-4-yl-piperidine-1-carboxamide

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 ~{N}-[(1~{R})-1-(3-methoxyphenyl)ethyl]-4-pyridin-4-yl-piperidine-1-carboxamide

Formula

C20 H25 N3 O2

Formal charge

0

Molecular weight

339.431 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 COc1cccc(c1)[CH](C)NC(=O)N2CCC(CC2)c3ccncc3
SMILES OpenEye OEToolkits 2.0.7 CC(c1cccc(c1)OC)NC(=O)N2CCC(CC2)c3ccncc3
Canonical SMILES CACTVS 3.385 COc1cccc(c1)[C@@H](C)NC(=O)N2CCC(CC2)c3ccncc3
Canonical SMILES OpenEye OEToolkits 2.0.7 C[C@H](c1cccc(c1)OC)NC(=O)N2CCC(CC2)c3ccncc3

IUPAC InChI

InChI=1S/C20H25N3O2/c1-15(18-4-3-5-19(14-18)25-2)22-20(24)23-12-8-17(9-13-23)16-6-10-21-11-7-16/h3-7,10-11,14-15,17H,8-9,12-13H2,1-2H3,(H,22,24)/t15-/m1/s1

IUPAC InChI key

TUPUYLLHTGZRRB-OAHLLOKOSA-N
5YS

wwPDB Information

Atom count

50 (25 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-07-19

Last modified at

2022-07-22

Status

Released

Obsoleted

Not Assigned



5YS : Atoms of Molecule

Total Number of Atoms: 50
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C2 C C1 N N N 0 -0.172 2.039 -0.351
2 C4 C C2 R N N 0 -2.562 1.57 -0.295
3 C6 C C3 N N N 0 -3.2 2.869 0.203
4 C7 C C4 N Y N 0 -3.401 0.398 0.147
5 C8 C C5 N Y N 0 -3.295 -0.079 1.44
6 C11 C C6 N Y N 0 -5.046 -1.278 -0.335
7 C16 C C7 N N N 0 1.32 1.061 1.326
8 C17 C C8 N N N 0 2.315 -0.062 1.015
9 C18 C C9 N N N 0 3.579 0.539 0.396
10 C19 C C10 N N N 0 3.221 1.243 -0.915
11 C21 C C11 N Y N 0 4.574 -0.559 0.12
12 C23 C C12 N Y N 0 5.198 -2.591 -0.967
13 O1 O O1 N N N 0 -0.363 2.756 -1.314
14 N3 N N1 N N N 0 -1.214 1.444 0.263
15 C9 C C13 N Y N 0 -4.062 -1.154 1.848
16 C14 C C16 N Y N 0 -4.278 -0.195 -0.74
17 C10 C C14 N Y N 0 -4.938 -1.754 0.964
18 O12 O O2 N N N 0 -5.906 -1.866 -1.206
19 C13 C C15 N N N 0 -6.669 -2.972 -0.719
20 N15 N N2 N N N 0 1.082 1.834 0.099
21 C20 C C17 N N N 0 2.236 2.381 -0.627
22 C22 C C18 N Y N 0 4.26 -1.602 -0.738
23 N24 N N3 N Y N 0 6.378 -2.551 -0.379
24 C25 C C19 N Y N 0 6.712 -1.572 0.438
25 C26 C C20 N Y N 0 5.826 -0.548 0.715
26 H1 H H1 N N N 0 -2.505 1.587 -1.383
27 H2 H H2 N N N 0 -4.204 2.963 -0.212
28 H3 H H3 N N N 0 -3.257 2.852 1.291
29 H4 H H4 N N N 0 -2.594 3.717 -0.116
30 H5 H H5 N N N 0 -2.611 0.389 2.133
31 H6 H H6 N N N 0 0.381 0.631 1.675
32 H7 H H7 N N N 0 1.734 1.714 2.095
33 H8 H H8 N N N 0 2.574 -0.583 1.937
34 H9 H H9 N N N 0 1.864 -0.764 0.314
35 H10 H H10 N N N 0 4.016 1.259 1.087
36 H11 H H11 N N N 0 4.125 1.65 -1.368
37 H12 H H12 N N N 0 2.761 0.529 -1.598
38 H13 H H13 N N N 0 4.959 -3.409 -1.63
39 H14 H H14 N N N 0 -1.071 0.932 1.074
40 H15 H H15 N N N 0 -3.978 -1.525 2.859
41 H16 H H16 N N N 0 -5.537 -2.594 1.283
42 H17 H H17 N N N 0 -5.994 -3.764 -0.394
43 H21 H H21 N N N 0 2.725 3.141 -0.017
44 H18 H H18 N N N 0 -7.281 -2.648 0.123
45 H19 H H19 N N N 0 -7.314 -3.347 -1.513
46 H20 H H20 N N N 0 -4.364 0.181 -1.749
47 H22 H H22 N N N 0 1.902 2.822 -1.566
48 H23 H H23 N N N 0 3.295 -1.641 -1.222
49 H24 H H24 N N N 0 7.688 -1.573 0.901
50 H25 H H25 N N N 0 6.106 0.252 1.385



5YS : Chemical Bonds

Total Number of Bonds: 52
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C6 C4 C C sing 1.53 N N
2 C8 C9 C C doub 1.38 N Y
3 C8 C7 C C sing 1.38 N Y
4 C9 C10 C C sing 1.38 N Y
5 C4 C7 C C sing 1.51 N N
6 C4 N3 C N sing 1.46 N N
7 C7 C14 C C doub 1.38 N Y
8 C10 C11 C C doub 1.39 N Y
9 C14 C11 C C sing 1.39 N Y
10 C11 O12 C O sing 1.36 N N
11 O12 C13 O C sing 1.43 N N
12 N3 C2 N C sing 1.35 N N
13 C16 C17 C C sing 1.53 N N
14 C16 N15 C N sing 1.47 N N
15 C2 O1 C O doub 1.22 N N
16 C2 N15 C N sing 1.35 N N
17 C17 C18 C C sing 1.53 N N
18 N15 C20 N C sing 1.47 N N
19 C22 C23 C C doub 1.38 N Y
20 C22 C21 C C sing 1.39 N Y
21 C23 N24 C N sing 1.32 N Y
22 C18 C21 C C sing 1.51 N N
23 C18 C19 C C sing 1.53 N N
24 C21 C26 C C doub 1.39 N Y
25 C19 C20 C C sing 1.53 N N
26 N24 C25 N C doub 1.32 N Y
27 C26 C25 C C sing 1.38 N Y
28 C4 H1 C H sing 1.09 N N
29 C6 H2 C H sing 1.09 N N
30 C6 H3 C H sing 1.09 N N
31 C6 H4 C H sing 1.09 N N
32 C8 H5 C H sing 1.08 N N
33 C16 H6 C H sing 1.09 N N
34 C16 H7 C H sing 1.09 N N
35 C17 H8 C H sing 1.09 N N
36 C17 H9 C H sing 1.09 N N
37 C18 H10 C H sing 1.09 N N
38 C19 H11 C H sing 1.09 N N
39 C19 H12 C H sing 1.09 N N
40 C23 H13 C H sing 1.08 N N
41 N3 H14 N H sing 0.97 N N
42 C9 H15 C H sing 1.08 N N
43 C10 H16 C H sing 1.08 N N
44 C13 H17 C H sing 1.09 N N
45 C13 H18 C H sing 1.09 N N
46 C13 H19 C H sing 1.09 N N
47 C14 H20 C H sing 1.08 N N
48 C20 H21 C H sing 1.09 N N
49 C20 H22 C H sing 1.09 N N
50 C22 H23 C H sing 1.08 N N
51 C25 H24 C H sing 1.08 N N
52 C26 H25 C H sing 1.08 N N



5YS : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
5YS 7p6n Open in New Window Bound ligand 8 1