Chemical Components in the PDB

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49O : Summary

Code

49O

One-letter code

X

Molecule name

2-(piperazin-1-yl)pyridine-3-carbonitrile

Systematic names

ProgramVersionName
ACDLabs 12.01 2-(piperazin-1-yl)pyridine-3-carbonitrile
OpenEye OEToolkits 1.9.2 2-piperazin-1-ylpyridine-3-carbonitrile

Formula

C10 H12 N4

Formal charge

0

Molecular weight

188.229 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 N#Cc1c(nccc1)N2CCNCC2
SMILES CACTVS 3.385 N#Cc1cccnc1N2CCNCC2
SMILES OpenEye OEToolkits 1.9.2 c1cc(c(nc1)N2CCNCC2)C#N
Canonical SMILES CACTVS 3.385 N#Cc1cccnc1N2CCNCC2
Canonical SMILES OpenEye OEToolkits 1.9.2 c1cc(c(nc1)N2CCNCC2)C#N

IUPAC InChI

InChI=1S/C10H12N4/c11-8-9-2-1-3-13-10(9)14-6-4-12-5-7-14/h1-3,12H,4-7H2

IUPAC InChI key

QSMNQUURWIAXAA-UHFFFAOYSA-N
49O

wwPDB Information

Atom count

26 (14 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2015-02-18

Last modified at

2015-05-01

Status

Released

Obsoleted

Not Assigned



49O : 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 C8 C C1 N N N 0 -1.293 -2.066 0.001
2 C12 C C2 N Y N 0 -3.24 1.092 0.002
3 C7 C C3 N Y N 0 -2.968 -0.264 0.001
4 C9 C C4 N Y N 0 -2.194 1.997 -0.003
5 C3 C C5 N Y N 0 -1.629 -0.674 0.001
6 C1 C C6 N Y N 0 -0.622 0.306 0.001
7 C10 C C7 N N N 0 2.836 -0.109 -1.21
8 C11 C C8 N N N 0 2.837 -0.102 1.211
9 C5 C C9 N N N 0 1.392 0.398 -1.21
10 C6 C C10 N N N 0 1.393 0.406 1.21
11 N13 N N1 N N N 0 -1.026 -3.17 0.001
12 N4 N N2 N Y N 0 -0.939 1.592 -0.004
13 N14 N N3 N N N 0 3.521 0.371 -0.002
14 N2 N N4 N N N 0 0.709 -0.074 0.002
15 H1 H H1 N N N 0 -4.262 1.442 0.001
16 H2 H H2 N N N 0 -3.768 -0.989 0.001
17 H3 H H3 N N N 0 -2.409 3.056 -0.007
18 H4 H H4 N N N 0 2.838 -1.199 -1.22
19 H5 H H5 N N N 0 3.353 0.264 -2.094
20 H6 H H6 N N N 0 3.356 0.277 2.092
21 H7 H H7 N N N 0 2.84 -1.192 1.228
22 H8 H H8 N N N 0 1.39 1.488 -1.228
23 H9 H H9 N N N 0 0.874 0.019 -2.091
24 H10 H H10 N N N 0 0.876 0.032 2.094
25 H11 H H11 N N N 0 1.391 1.496 1.22
26 H12 H H12 N N N 0 3.597 1.377 -0.005



49O : Chemical Bonds

Total Number of Bonds: 27
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N14 C11 N C sing 1.47 N N
2 N14 C10 N C sing 1.47 N N
3 C11 C6 C C sing 1.53 N N
4 C10 C5 C C sing 1.53 N N
5 C6 N2 C N sing 1.47 N N
6 C5 N2 C N sing 1.47 N N
7 N13 C8 N C trip 1.14 N N
8 N2 C1 N C sing 1.38 N N
9 C8 C3 C C sing 1.43 N N
10 C1 C3 C C doub 1.41 N Y
11 C1 N4 C N sing 1.32 N Y
12 C3 C7 C C sing 1.4 N Y
13 N4 C9 N C doub 1.32 N Y
14 C7 C12 C C doub 1.38 N Y
15 C9 C12 C C sing 1.38 N Y
16 C12 H1 C H sing 1.08 N N
17 C7 H2 C H sing 1.08 N N
18 C9 H3 C H sing 1.08 N N
19 C10 H4 C H sing 1.09 N N
20 C10 H5 C H sing 1.09 N N
21 C11 H6 C H sing 1.09 N N
22 C11 H7 C H sing 1.09 N N
23 C5 H8 C H sing 1.09 N N
24 C5 H9 C H sing 1.09 N N
25 C6 H10 C H sing 1.09 N N
26 C6 H11 C H sing 1.09 N N
27 N14 H12 N H sing 1.01 N N



49O : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
49O 4y2r Open in New Window Bound ligand 1 1