Chemical Components in the PDB

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O8G : Summary

Code

O8G

One-letter code

X

Molecule name

1-(azidoacetyl)-4-(3-thiophen-2-yl-1,2,4-oxadiazol-5-yl)piperidine

Systematic names

ProgramVersionName
ACDLabs 12.01 2-azido-1-{4-[3-(thiophen-2-yl)-1,2,4-oxadiazol-5-yl]piperidin-1-yl}ethanone
OpenEye OEToolkits 1.7.0 2-azido-1-[4-(3-thiophen-2-yl-1,2,4-oxadiazol-5-yl)piperidin-1-yl]ethanone

Formula

C13 H14 N6 O2 S

Formal charge

0

Molecular weight

318.354 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 [N-]=[N+]=N\CC(=O)N3CCC(c1onc(n1)c2sccc2)CC3
SMILES CACTVS 3.370 [N-]=[N+]=NCC(=O)N1CCC(CC1)c2onc(n2)c3sccc3
SMILES OpenEye OEToolkits 1.7.0 c1cc(sc1)c2nc(on2)C3CCN(CC3)C(=O)CN=[N+]=[N-]
Canonical SMILES CACTVS 3.370 [N-]=[N+]=NCC(=O)N1CCC(CC1)c2onc(n2)c3sccc3
Canonical SMILES OpenEye OEToolkits 1.7.0 c1cc(sc1)c2nc(on2)C3CCN(CC3)C(=O)CN=[N+]=[N-]

IUPAC InChI

InChI=1S/C13H14N6O2S/c14-18-15-8-11(20)19-5-3-9(4-6-19)13-16-12(17-21-13)10-2-1-7-22-10/h1-2,7,9H,3-6,8H2

IUPAC InChI key

RJFYHVFZGWNOBV-UHFFFAOYSA-N
O8G

wwPDB Information

Atom count

36 (22 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2010-08-05

Last modified at

2021-03-13

Status

Released

Obsoleted

Not Assigned



O8G : Atoms of Molecule

Total Number of Atoms: 36
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 -0.92 -1.02 1.198
2 C4 C C4 N N N 0 -2.225 -1.788 0.965
3 N7 N N7 N N N 0 -3.019 -1.075 -0.045
4 C8 C C8 N N N 0 -2.395 -0.754 -1.336
5 C11 C C11 N N N 0 -1.088 0.002 -1.078
6 C14 C C14 N N N 0 -0.203 -0.823 -0.14
7 C16 C C16 N N N 0 -4.295 -0.723 0.207
8 O17 O O17 N N N 0 -4.799 -0.994 1.276
9 C18 C C18 N N N 0 -5.096 0.007 -0.84
10 N21 N N21 N Y N 0 2.296 -0.542 -0.199
11 C22 C C22 N Y N 0 1.098 -0.098 0.09
12 O23 O O23 N Y N 0 1.245 1.118 0.625
13 N24 N N24 N Y N 0 2.42 1.414 0.67
14 C25 C C25 N Y N 0 3.147 0.44 0.179
15 C26 C C26 N Y N 0 4.62 0.419 0.06
16 C27 C C27 N Y N 0 5.447 1.41 0.45
17 C29 C C29 N Y N 0 6.786 1.161 0.237
18 C31 C C31 N Y N 0 7.06 -0.023 -0.322
19 S33 S S33 N Y N 0 5.566 -0.906 -0.605
20 N34 N N34 N N N 0 -6.442 0.274 -0.327
21 H1A H H1A N N N 0 -0.28 -1.587 1.873
22 N36 N N36 N N N 1 -6.81 1.333 -0.237
23 N37 N N37 N N N -1 -7.178 2.391 -0.148
24 H1 H H1 N N N 0 -1.143 -0.048 1.638
25 H4 H H4 N N N 0 -2.0 -2.793 0.61
26 H4A H H4A N N N 0 -2.787 -1.844 1.898
27 H8 H H8 N N N 0 -2.183 -1.676 -1.879
28 H8A H H8A N N N 0 -3.069 -0.129 -1.923
29 H11 H H11 N N N 0 -0.567 0.162 -2.022
30 H11A H H11A N N N 0 -1.309 0.964 -0.617
31 H14 H H14 N N N 0 -0.003 -1.795 -0.591
32 H18 H H18 N N N 0 -4.606 0.951 -1.081
33 H18A H H18A N N N 0 -5.165 -0.606 -1.739
34 H27 H H27 N N N 0 5.089 2.328 0.893
35 H29 H H29 N N N 0 7.557 1.869 0.502
36 H31 H H31 N N N 0 8.05 -0.383 -0.56



O8G : Chemical Bonds

Total Number of Bonds: 38
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C14 C C sing 1.53 N N
2 C1 H1 C H sing 1.09 N N
3 C1 H1A C H sing 1.09 N N
4 C4 C1 C C sing 1.53 N N
5 C4 N7 C N sing 1.47 N N
6 C4 H4 C H sing 1.09 N N
7 C4 H4A C H sing 1.09 N N
8 N7 C8 N C sing 1.47 N N
9 C8 C11 C C sing 1.53 N N
10 C8 H8 C H sing 1.09 N N
11 C8 H8A C H sing 1.09 N N
12 C11 H11 C H sing 1.09 N N
13 C11 H11A C H sing 1.09 N N
14 C14 C11 C C sing 1.53 N N
15 C14 C22 C C sing 1.51 N N
16 C14 H14 C H sing 1.09 N N
17 C16 N7 C N sing 1.35 N N
18 C16 C18 C C sing 1.51 N N
19 O17 C16 O C doub 1.21 N N
20 C18 H18 C H sing 1.09 N N
21 C18 H18A C H sing 1.09 N N
22 N21 C22 N C doub 1.31 N Y
23 N21 C25 N C sing 1.35 N Y
24 C22 O23 C O sing 1.34 N Y
25 O23 N24 O N sing 1.21 N Y
26 C25 N24 C N doub 1.31 N Y
27 C26 C25 C C sing 1.48 N Y
28 C26 S33 C S sing 1.76 N Y
29 C27 C26 C C doub 1.35 N Y
30 C27 C29 C C sing 1.38 N Y
31 C27 H27 C H sing 1.08 N N
32 C29 C31 C C doub 1.34 N Y
33 C29 H29 C H sing 1.08 N N
34 C31 S33 C S sing 1.76 N Y
35 C31 H31 C H sing 1.08 N N
36 N34 C18 N C sing 1.46 N N
37 N36 N34 N N doub 1.12 N N
38 N37 N36 N N doub 1.12 N N



O8G : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
O8G 3o8g Open in New Window Bound ligand 1 1