Chemical Components in the PDB

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D4V : Summary

Code

D4V

One-letter code

X

Molecule name

3-methylpyridin-2-ol

Systematic names

ProgramVersionName
ACDLabs 12.01 3-methylpyridin-2-ol
OpenEye OEToolkits 2.0.6 3-methylpyridin-2-ol

Formula

C6 H7 N O

Formal charge

0

Molecular weight

109.126 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 c1nc(O)c(cc1)C
SMILES CACTVS 3.385 Cc1cccnc1O
SMILES OpenEye OEToolkits 2.0.6 Cc1cccnc1O
Canonical SMILES CACTVS 3.385 Cc1cccnc1O
Canonical SMILES OpenEye OEToolkits 2.0.6 Cc1cccnc1O

IUPAC InChI

InChI=1S/C6H7NO/c1-5-3-2-4-7-6(5)8/h2-4H,1H3,(H,7,8)

IUPAC InChI key

MVKDNXIKAWKCCS-UHFFFAOYSA-N
D4V

wwPDB Information

Atom count

15 (8 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-10-18

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



D4V : Atoms of Molecule

Total Number of Atoms: 15
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 1.842 0.65 0.0
2 C5 C C2 N Y N 0 -0.464 0.687 0.018
3 C3 C C3 N Y N 0 1.86 -0.73 -0.014
4 C2 C C4 N Y N 0 0.657 -1.424 -0.011
5 C1 C C5 N Y N 0 -0.522 -0.701 0.005
6 O O O1 N N N 0 -1.613 1.407 0.035
7 C C C6 N N N 0 -1.852 -1.41 0.009
8 N N N1 N Y N 0 0.701 1.312 0.015
9 H5 H H1 N N N 0 2.775 1.195 0.002
10 H4 H H2 N N N 0 2.798 -1.264 -0.027
11 H3 H H3 N N N 0 0.643 -2.504 -0.022
12 H1 H H4 N N N 0 -2.164 -1.59 1.038
13 H2 H H5 N N N 0 -2.595 -0.79 -0.493
14 H H H6 N N N 0 -1.759 -2.361 -0.514
15 H7 H H7 N N N 0 -1.954 1.625 -0.843



D4V : Chemical Bonds

Total Number of Bonds: 15
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C2 C3 C C sing 1.39 N Y
2 C2 C1 C C doub 1.38 N Y
3 C3 C4 C C doub 1.38 N Y
4 C C1 C C sing 1.51 N N
5 C1 C5 C C sing 1.39 N Y
6 C4 N C N sing 1.32 N Y
7 C5 N C N doub 1.32 N Y
8 C5 O C O sing 1.36 N N
9 C4 H5 C H sing 1.08 N N
10 C3 H4 C H sing 1.08 N N
11 C2 H3 C H sing 1.08 N N
12 C H1 C H sing 1.09 N N
13 C H2 C H sing 1.09 N N
14 C H C H sing 1.09 N N
15 O H7 O H sing 0.97 N N



D4V : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
D4V 5s8h Open in New Window Bound ligand 1 1
D4V 6bb7 Open in New Window Bound ligand 1 1