Chemical Components in the PDB

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Z5H : Summary

Code

Z5H

One-letter code

X

Molecule name

N-methyl-1-{3-[1-(4-methylphenyl)cyclopentyl]-1,2,4-oxadiazol-5-yl}-N-[(thiophen-2-yl)methyl]methanamine

Systematic names

ProgramVersionName
ACDLabs 12.01 N-methyl-1-{3-[1-(4-methylphenyl)cyclopentyl]-1,2,4-oxadiazol-5-yl}-N-[(thiophen-2-yl)methyl]methanamine
OpenEye OEToolkits 2.0.7 ~{N}-methyl-~{N}-[[3-[1-(4-methylphenyl)cyclopentyl]-1,2,4-oxadiazol-5-yl]methyl]-1-thiophen-2-yl-methanamine

Formula

C21 H25 N3 O S

Formal charge

0

Molecular weight

367.508 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 CN(Cc1nc(no1)C1(CCCC1)c1ccc(C)cc1)Cc1cccs1
SMILES CACTVS 3.385 CN(Cc1onc(n1)C2(CCCC2)c3ccc(C)cc3)Cc4sccc4
SMILES OpenEye OEToolkits 2.0.7 Cc1ccc(cc1)C2(CCCC2)c3nc(on3)CN(C)Cc4cccs4
Canonical SMILES CACTVS 3.385 CN(Cc1onc(n1)C2(CCCC2)c3ccc(C)cc3)Cc4sccc4
Canonical SMILES OpenEye OEToolkits 2.0.7 Cc1ccc(cc1)C2(CCCC2)c3nc(on3)CN(C)Cc4cccs4

IUPAC InChI

InChI=1S/C21H25N3OS/c1-16-7-9-17(10-8-16)21(11-3-4-12-21)20-22-19(25-23-20)15-24(2)14-18-6-5-13-26-18/h5-10,13H,3-4,11-12,14-15H2,1-2H3

IUPAC InChI key

GPXYCFQNEZDPGQ-UHFFFAOYSA-N
Z5H

wwPDB Information

Atom count

51 (26 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2023-03-06

Last modified at

2023-09-29

Status

Released

Obsoleted

Not Assigned



Z5H : Atoms of Molecule

Total Number of Atoms: 51
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C01 C C1 N Y N 0 -1.66 2.742 0.233
2 C02 C C2 N Y N 0 -1.778 1.365 0.243
3 C03 C C3 N Y N 0 -3.017 0.776 0.068
4 C04 C C4 N Y N 0 -4.137 1.564 -0.117
5 C05 C C5 N Y N 0 -4.019 2.942 -0.127
6 C06 C C6 N Y N 0 -2.782 3.531 0.053
7 C07 C C7 N N N 0 -2.653 5.032 0.042
8 C08 C C8 N N N 0 -3.145 -0.725 0.079
9 C09 C C9 N N N 0 -3.995 -1.173 1.281
10 C10 C C10 N N N 0 -5.224 -1.905 0.704
11 C11 C C11 N N N 0 -4.759 -2.383 -0.695
12 C12 C C12 N N N 0 -3.886 -1.201 -1.188
13 C13 C C13 N Y N 0 -1.78 -1.36 0.147
14 C14 C C14 N Y N 0 0.209 -1.931 -0.294
15 C15 C C15 N N N 0 1.563 -2.096 -0.935
16 C16 C C16 N N N 0 3.857 -1.326 -0.845
17 C17 C C17 N Y N 0 4.789 -0.394 -0.113
18 C18 C C18 N N N 0 2.042 0.277 -0.862
19 C19 C C19 N Y N 0 5.365 -0.649 1.062
20 C20 C C20 N Y N 0 6.274 1.431 0.754
21 C21 C C21 N Y N 0 6.185 0.358 1.541
22 N01 N N1 N Y N 0 -1.348 -2.159 1.076
23 N02 N N2 N Y N 0 -0.786 -1.207 -0.747
24 N03 N N3 N N N 0 2.473 -1.059 -0.43
25 O01 O O1 N Y N 0 -0.207 -2.497 0.842
26 S01 S S1 N Y N 0 5.29 1.192 -0.684
27 H17 H H1 N N N 0 -0.693 3.203 0.369
28 H18 H H2 N N N 0 -0.903 0.749 0.387
29 H19 H H3 N N N 0 -5.104 1.104 -0.254
30 H16 H H4 N N N 0 -4.894 3.558 -0.272
31 H03 H H5 N N N 0 -2.474 5.374 -0.977
32 H02 H H6 N N N 0 -3.573 5.479 0.418
33 H01 H H7 N N N 0 -1.819 5.33 0.677
34 H05 H H8 N N N 0 -3.42 -1.85 1.913
35 H04 H H9 N N N 0 -4.314 -0.304 1.857
36 H06 H H10 N N N 0 -5.489 -2.758 1.33
37 H07 H H11 N N N 0 -6.068 -1.222 0.615
38 H08 H H12 N N N 0 -4.166 -3.293 -0.614
39 H09 H H13 N N N 0 -5.614 -2.537 -1.353
40 H10 H H14 N N N 0 -4.514 -0.403 -1.585
41 H11 H H15 N N N 0 -3.175 -1.54 -1.941
42 H12 H H16 N N N 0 1.963 -3.08 -0.693
43 H13 H H17 N N N 0 1.467 -1.999 -2.017
44 H15 H H18 N N N 0 3.951 -1.165 -1.919
45 H14 H H19 N N N 0 4.115 -2.358 -0.608
46 H20 H H20 N N N 0 1.04 0.476 -0.481
47 H21 H H21 N N N 0 2.733 1.025 -0.474
48 H22 H H22 N N N 0 2.033 0.321 -1.951
49 H25 H H23 N N N 0 5.204 -1.572 1.6
50 H23 H H24 N N N 0 6.864 2.311 0.966
51 H24 H H25 N N N 0 6.711 0.281 2.481



Z5H : Chemical Bonds

Total Number of Bonds: 54
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C07 C06 C C sing 1.51 N N
2 C06 C01 C C doub 1.38 N Y
3 C06 C05 C C sing 1.38 N Y
4 C01 C02 C C sing 1.38 N Y
5 C05 C04 C C doub 1.38 N Y
6 C02 C03 C C doub 1.38 N Y
7 C04 C03 C C sing 1.38 N Y
8 C03 C08 C C sing 1.51 N N
9 C12 C08 C C sing 1.54 N N
10 C12 C11 C C sing 1.55 N N
11 C08 C13 C C sing 1.51 N N
12 C08 C09 C C sing 1.54 N N
13 N02 C13 N C sing 1.35 N Y
14 N02 C14 N C doub 1.31 N Y
15 C18 N03 C N sing 1.47 N N
16 C13 N01 C N doub 1.3 N Y
17 C15 C14 C C sing 1.51 N N
18 C15 N03 C N sing 1.47 N N
19 C14 O01 C O sing 1.34 N Y
20 C09 C10 C C sing 1.54 N N
21 C11 C10 C C sing 1.55 N N
22 N03 C16 N C sing 1.47 N N
23 N01 O01 N O sing 1.21 N Y
24 C16 C17 C C sing 1.51 N N
25 C17 C19 C C doub 1.33 N Y
26 C17 S01 C S sing 1.76 N Y
27 C19 C21 C C sing 1.38 N Y
28 S01 C20 S C sing 1.76 N Y
29 C21 C20 C C doub 1.33 N Y
30 C01 H17 C H sing 1.08 N N
31 C02 H18 C H sing 1.08 N N
32 C04 H19 C H sing 1.08 N N
33 C05 H16 C H sing 1.08 N N
34 C07 H03 C H sing 1.09 N N
35 C07 H02 C H sing 1.09 N N
36 C07 H01 C H sing 1.09 N N
37 C09 H05 C H sing 1.09 N N
38 C09 H04 C H sing 1.09 N N
39 C10 H06 C H sing 1.09 N N
40 C10 H07 C H sing 1.09 N N
41 C11 H08 C H sing 1.09 N N
42 C11 H09 C H sing 1.09 N N
43 C12 H10 C H sing 1.09 N N
44 C12 H11 C H sing 1.09 N N
45 C15 H12 C H sing 1.09 N N
46 C15 H13 C H sing 1.09 N N
47 C16 H15 C H sing 1.09 N N
48 C16 H14 C H sing 1.09 N N
49 C18 H20 C H sing 1.09 N N
50 C18 H21 C H sing 1.09 N N
51 C18 H22 C H sing 1.09 N N
52 C19 H25 C H sing 1.08 N N
53 C20 H23 C H sing 1.08 N N
54 C21 H24 C H sing 1.08 N N



Z5H : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
Z5H 8gd2 Open in New Window Bound ligand 1 1