Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

RDJ : Summary

Code

RDJ

One-letter code

X

Molecule name

N-ethyl-2-{[5-(propan-2-yl)-1,3,4-oxadiazol-2-yl]sulfanyl}acetamide

Systematic names

ProgramVersionName
ACDLabs 12.01 N-ethyl-2-{[5-(propan-2-yl)-1,3,4-oxadiazol-2-yl]sulfanyl}acetamide
OpenEye OEToolkits 2.0.6 ~{N}-ethyl-2-[(5-propan-2-yl-1,3,4-oxadiazol-2-yl)sulfanyl]ethanamide

Formula

C9 H15 N3 O2 S

Formal charge

0

Molecular weight

229.299 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 c1(SCC(=O)NCC)nnc(o1)C(C)C
SMILES CACTVS 3.385 CCNC(=O)CSc1oc(nn1)C(C)C
SMILES OpenEye OEToolkits 2.0.6 CCNC(=O)CSc1nnc(o1)C(C)C
Canonical SMILES CACTVS 3.385 CCNC(=O)CSc1oc(nn1)C(C)C
Canonical SMILES OpenEye OEToolkits 2.0.6 CCNC(=O)CSc1nnc(o1)C(C)C

IUPAC InChI

InChI=1S/C9H15N3O2S/c1-4-10-7(13)5-15-9-12-11-8(14-9)6(2)3/h6H,4-5H2,1-3H3,(H,10,13)

IUPAC InChI key

DWIDCIXKOJCTSJ-UHFFFAOYSA-N
RDJ

wwPDB Information

Atom count

30 (15 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-02-10

Last modified at

2020-05-29

Status

Released

Obsoleted

Not Assigned



RDJ : Atoms of Molecule

Total Number of Atoms: 30
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C1 N Y N 0 1.063 -0.373 0.001
2 C5 C C2 N Y N 0 3.179 0.039 0.001
3 C6 C C3 N N N 0 4.678 -0.118 0.001
4 N1 N N1 N Y N 0 1.26 0.924 -0.001
5 C7 C C4 N N N 0 5.26 0.546 -1.248
6 C8 C C5 N N N 0 5.26 0.548 1.25
7 N2 N N2 N Y N 0 2.524 1.163 -0.001
8 O O O1 N N N 0 -3.282 -1.422 0.001
9 C2 C C6 N N N 0 -3.035 -0.235 0.0
10 N N N3 N N N 0 -4.042 0.662 0.0
11 C1 C C7 N N N 0 -5.432 0.202 0.0
12 C C C8 N N N 0 -6.369 1.412 -0.001
13 C3 C C9 N N N 0 -1.605 0.238 0.0
14 S S S1 N N N 0 -0.496 -1.193 0.001
15 O1 O O2 N Y N 0 2.274 -0.96 -0.004
16 H1 H H1 N N N 0 4.933 -1.178 0.002
17 H2 H H2 N N N 0 4.846 0.072 -2.138
18 H3 H H3 N N N 0 5.006 1.606 -1.249
19 H4 H H4 N N N 0 6.345 0.433 -1.248
20 H5 H H5 N N N 0 4.845 0.075 2.14
21 H6 H H6 N N N 0 6.344 0.434 1.25
22 H7 H H7 N N N 0 5.005 1.607 1.249
23 H8 H H8 N N N 0 -3.845 1.612 -0.001
24 H9 H H9 N N N 0 -5.616 -0.4 -0.89
25 H10 H H10 N N N 0 -5.616 -0.399 0.891
26 H11 H H11 N N N 0 -6.186 2.015 0.889
27 H12 H H12 N N N 0 -6.186 2.013 -0.891
28 H13 H H13 N N N 0 -7.404 1.07 -0.001
29 H14 H H14 N N N 0 -1.421 0.839 -0.89
30 H15 H H15 N N N 0 -1.421 0.84 0.89



RDJ : Chemical Bonds

Total Number of Bonds: 30
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C8 C6 C C sing 1.53 N N
2 C7 C6 C C sing 1.53 N N
3 C6 C5 C C sing 1.51 N N
4 C C1 C C sing 1.53 N N
5 C5 N2 C N doub 1.3 N Y
6 C5 O1 C O sing 1.35 N Y
7 N2 N1 N N sing 1.29 N Y
8 C1 N C N sing 1.46 N N
9 O1 C4 O C sing 1.35 N Y
10 N1 C4 N C doub 1.31 N Y
11 N C2 N C sing 1.35 N N
12 C4 S C S sing 1.76 N N
13 O C2 O C doub 1.21 N N
14 C2 C3 C C sing 1.51 N N
15 C3 S C S sing 1.81 N N
16 C6 H1 C H sing 1.09 N N
17 C7 H2 C H sing 1.09 N N
18 C7 H3 C H sing 1.09 N N
19 C7 H4 C H sing 1.09 N N
20 C8 H5 C H sing 1.09 N N
21 C8 H6 C H sing 1.09 N N
22 C8 H7 C H sing 1.09 N N
23 N H8 N H sing 0.97 N N
24 C1 H9 C H sing 1.09 N N
25 C1 H10 C H sing 1.09 N N
26 C H11 C H sing 1.09 N N
27 C H12 C H sing 1.09 N N
28 C H13 C H sing 1.09 N N
29 C3 H14 C H sing 1.09 N N
30 C3 H15 C H sing 1.09 N N



RDJ : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
RDJ 5r28 Open in New Window Bound ligand 1 1
RDJ 5rca Open in New Window Bound ligand 1 1
RDJ 8ohj Open in New Window Bound ligand 1 1