Chemical Components in the PDB

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WOD : Summary

Code

WOD

One-letter code

X

Molecule name

3-cyclopropyl-5-[(3R)-pyrrolidin-3-yl]-1,2,4-oxadiazole

Systematic names

ProgramVersionName
ACDLabs 12.01 3-cyclopropyl-5-[(3R)-pyrrolidin-3-yl]-1,2,4-oxadiazole
OpenEye OEToolkits 2.0.7 3-cyclopropyl-5-[(3~{R})-pyrrolidin-3-yl]-1,2,4-oxadiazole

Formula

C9 H13 N3 O

Formal charge

0

Molecular weight

179.219 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C1C(CNC1)c3onc(C2CC2)n3
SMILES CACTVS 3.385 C1C[CH](CN1)c2onc(n2)C3CC3
SMILES OpenEye OEToolkits 2.0.7 C1CC1c2nc(on2)C3CCNC3
Canonical SMILES CACTVS 3.385 C1C[C@H](CN1)c2onc(n2)C3CC3
Canonical SMILES OpenEye OEToolkits 2.0.7 C1CNC[C@@H]1c2nc(no2)C3CC3

IUPAC InChI

InChI=1S/C9H13N3O/c1-2-6(1)8-11-9(13-12-8)7-3-4-10-5-7/h6-7,10H,1-5H2/t7-/m1/s1

IUPAC InChI key

UHWKRAJPWOGTQP-SSDOTTSWSA-N
WOD

wwPDB Information

Atom count

26 (13 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-10-30

Last modified at

2020-11-06

Status

Released

Obsoleted

Not Assigned



WOD : Atoms of Molecule

Total Number of Atoms: 26
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C10 C C1 N N N 0 2.588 -0.766 -0.956
2 N12 N N1 N N N 0 3.877 0.527 0.598
3 C13 C C2 N N N 0 2.49 1.064 0.67
4 C01 C C3 N N N 0 -4.108 0.77 0.55
5 C02 C C4 N N N 0 -4.225 -0.685 0.09
6 C03 C C5 N N N 0 -3.211 0.249 -0.574
7 C04 C C6 N Y N 0 -1.753 0.032 -0.257
8 C07 C C7 N Y N 0 0.36 0.148 -0.274
9 C09 C C8 R N N 0 1.791 0.502 -0.586
10 C11 C C9 N N N 0 3.704 -0.864 0.107
11 N05 N N2 N Y N 0 -1.274 -0.771 0.645
12 N08 N N3 N Y N 0 -0.71 0.628 -0.861
13 O06 O O1 N Y N 0 -0.062 -0.717 0.653
14 H1 H H1 N N N 0 1.945 -1.644 -0.911
15 H2 H H2 N N N 0 3.021 -0.664 -1.951
16 H3 H H3 N N N 0 4.44 1.069 -0.04
17 H5 H H5 N N N 0 1.992 0.71 1.572
18 H6 H H6 N N N 0 2.503 2.154 0.644
19 H7 H H7 N N N 0 -4.914 1.45 0.276
20 H8 H H8 N N N 0 -3.644 0.955 1.519
21 H9 H H9 N N N 0 -3.838 -1.456 0.756
22 H10 H H10 N N N 0 -5.107 -0.961 -0.487
23 H11 H H11 N N N 0 -3.426 0.587 -1.588
24 H12 H H12 N N N 0 1.833 1.227 -1.399
25 H13 H H13 N N N 0 3.395 -1.52 0.921
26 H14 H H14 N N N 0 4.629 -1.225 -0.344



WOD : Chemical Bonds

Total Number of Bonds: 28
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C01 C02 C C sing 1.53 N N
2 C01 C03 C C sing 1.53 N N
3 C13 N12 C N sing 1.49 N N
4 C13 C09 C C sing 1.54 N N
5 N12 C11 N C sing 1.49 N N
6 C02 C03 C C sing 1.53 N N
7 C03 C04 C C sing 1.51 N N
8 N08 C04 N C sing 1.34 N Y
9 N08 C07 N C doub 1.31 N Y
10 C09 C07 C C sing 1.51 N N
11 C09 C10 C C sing 1.54 N N
12 C11 C10 C C sing 1.54 N N
13 C04 N05 C N doub 1.3 N Y
14 C07 O06 C O sing 1.34 N Y
15 N05 O06 N O sing 1.21 N Y
16 C10 H1 C H sing 1.09 N N
17 C10 H2 C H sing 1.09 N N
18 N12 H3 N H sing 1.01 N N
19 C13 H5 C H sing 1.09 N N
20 C13 H6 C H sing 1.09 N N
21 C01 H7 C H sing 1.09 N N
22 C01 H8 C H sing 1.09 N N
23 C02 H9 C H sing 1.09 N N
24 C02 H10 C H sing 1.09 N N
25 C03 H11 C H sing 1.09 N N
26 C09 H12 C H sing 1.09 N N
27 C11 H13 C H sing 1.09 N N
28 C11 H14 C H sing 1.09 N N



WOD : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
WOD 5ryj Open in New Window Bound ligand 1 1