Chemical Components in the PDB

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0PY : Summary

Code

0PY

One-letter code

X

Molecule name

pyridine

Synonyms

Azabenzene
Azine

Systematic names

ProgramVersionName
ACDLabs 10.04 pyridine
OpenEye OEToolkits 1.5.0 pyridine

Formula

C5 H5 N

Formal charge

0

Molecular weight

79.1 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 n1ccccc1
SMILES CACTVS 3.341 c1ccncc1
SMILES OpenEye OEToolkits 1.5.0 c1ccncc1
Canonical SMILES CACTVS 3.341 c1ccncc1
Canonical SMILES OpenEye OEToolkits 1.5.0 c1ccncc1

IUPAC InChI

InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H

IUPAC InChI key

JUJWROOIHBZHMG-UHFFFAOYSA-N
0PY

wwPDB Information

Atom count

11 (6 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2009-04-09

Last modified at

2020-05-26

Status

Released

Obsoleted

Not Assigned



0PY : Atoms of Molecule

Total Number of Atoms: 11
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C5 C C5 N Y N 0 -1.152 0.697 -0.0020
2 N1 N N1 N Y N 0 -0.0010 1.34 0.0010
3 C4 C C4 N Y N 0 -1.191 -0.684 0.0010
4 C3 C C3 N Y N 0 0.0010 -1.393 0.0010
5 C2 C C2 N Y N 0 1.191 -0.683 -0.0020
6 C1 C C1 N Y N 0 1.152 0.698 0.0010
7 H5 H H5 N N N 0 -2.076 1.257 -0.0020
8 H4 H H4 N N N 0 -2.137 -1.205 0.0030
9 H3 H H3 N N N 0 0.0010 -2.473 0.0030
10 H2 H H2 N N N 0 2.138 -1.203 -0.0020
11 H1 H H1 N N N 0 2.075 1.259 -0.0010



0PY : Chemical Bonds

Total Number of Bonds: 11
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C4 C5 C C doub 1.38 N Y
2 N1 C5 N C sing 1.32 N Y
3 C5 H5 C H sing 1.08 N N
4 C1 N1 C N doub 1.32 N Y
5 C3 C4 C C sing 1.39 N Y
6 C4 H4 C H sing 1.08 N N
7 C2 C3 C C doub 1.39 N Y
8 C3 H3 C H sing 1.08 N N
9 C2 C1 C C sing 1.38 N Y
10 C2 H2 C H sing 1.08 N N
11 C1 H1 C H sing 1.08 N N



0PY : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
0PY 3gup Open in New Window Bound ligand 3 1
0PY 3v36 Open in New Window Bound ligand 1 1
0PY 6jzs Open in New Window Bound ligand 3 1