Chemical Components in the PDB

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0OM : Summary

Code

0OM

One-letter code

X

Molecule name

benzyl pyridine-3-carboxylate

Synonyms

Benzyl nicotinate

Systematic names

ProgramVersionName
ACDLabs 12.01 benzyl pyridine-3-carboxylate
OpenEye OEToolkits 1.7.6 (phenylmethyl) pyridine-3-carboxylate

Formula

C13 H11 N O2

Formal charge

0

Molecular weight

213.232 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(OCc1ccccc1)c2cccnc2
SMILES CACTVS 3.370 O=C(OCc1ccccc1)c2cccnc2
SMILES OpenEye OEToolkits 1.7.6 c1ccc(cc1)COC(=O)c2cccnc2
Canonical SMILES CACTVS 3.370 O=C(OCc1ccccc1)c2cccnc2
Canonical SMILES OpenEye OEToolkits 1.7.6 c1ccc(cc1)COC(=O)c2cccnc2

IUPAC InChI

InChI=1S/C13H11NO2/c15-13(12-7-4-8-14-9-12)16-10-11-5-2-1-3-6-11/h1-9H,10H2

IUPAC InChI key

KVYGGMBOZFWZBQ-UHFFFAOYSA-N
0OM

wwPDB Information

Atom count

27 (16 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-04-03

Last modified at

2012-11-30

Status

Released

Obsoleted

Not Assigned



0OM : Atoms of Molecule

Total Number of Atoms: 27
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 CAB C CAB N Y N 0 -4.822 1.087 0.0020
2 CAC C CAC N Y N 0 -4.252 0.694 1.199
3 CAD C CAD N Y N 0 -4.245 0.71 -1.196
4 CAE C CAE N Y N 0 4.712 0.013 0.0010
5 CAF C CAF N Y N 0 4.551 1.387 0.0050
6 CAG C CAG N Y N 0 -3.103 -0.075 1.197
7 CAH C CAH N Y N 0 -3.096 -0.059 -1.197
8 CAI C CAI N Y N 0 3.592 -0.8 -0.0010
9 CAJ C CAJ N Y N 0 2.254 1.201 -0.0020
10 CAK C CAK N N N 0 -1.27 -1.285 -0.0030
11 CAN C CAN N N N 0 1.102 -1.013 -0.0020
12 CAO C CAO N Y N 0 -2.522 -0.447 -0.0010
13 CAP C CAP N Y N 0 2.331 -0.193 0.0
14 H1 H H1 N N N 0 -2.657 -0.381 2.131
15 H10 H H10 N N N 0 5.423 2.024 0.0070
16 H11 H H11 N N N 0 1.288 1.684 -0.0010
17 H2 H H2 N N N 0 -4.703 0.988 2.134
18 H3 H H3 N N N 0 -5.72 1.687 0.0040
19 H4 H H4 N N N 0 -4.691 1.016 -2.13
20 H5 H H5 N N N 0 -2.645 -0.354 -2.134
21 H6 H H6 N N N 0 -1.254 -1.916 0.885
22 H7 H H7 N N N 0 -1.253 -1.912 -0.895
23 H8 H H8 N N N 0 3.69 -1.876 -0.0030
24 H9 H H9 N N N 0 5.701 -0.42 0.0010
25 NAL N NAL N Y N 0 3.349 1.932 0.0060
26 OAA O OAA N N N 0 1.181 -2.225 -0.0050
27 OAM O OAM N N N 0 -0.106 -0.417 -0.0010



0OM : 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 NAL CAJ N C doub 1.32 N Y
2 NAL CAF N C sing 1.32 N Y
3 CAJ CAP C C sing 1.4 N Y
4 OAA CAN O C doub 1.21 N N
5 CAF CAE C C doub 1.38 N Y
6 CAP CAN C C sing 1.48 N N
7 CAP CAI C C doub 1.4 N Y
8 CAN OAM C O sing 1.35 N N
9 CAE CAI C C sing 1.38 N Y
10 OAM CAK O C sing 1.45 N N
11 CAK CAO C C sing 1.51 N N
12 CAO CAH C C doub 1.38 N Y
13 CAO CAG C C sing 1.38 N Y
14 CAH CAD C C sing 1.38 N Y
15 CAG CAC C C doub 1.38 N Y
16 CAD CAB C C doub 1.38 N Y
17 CAC CAB C C sing 1.38 N Y
18 CAG H1 C H sing 1.08 N N
19 CAC H2 C H sing 1.08 N N
20 CAB H3 C H sing 1.08 N N
21 CAD H4 C H sing 1.08 N N
22 CAH H5 C H sing 1.08 N N
23 CAK H6 C H sing 1.09 N N
24 CAK H7 C H sing 1.09 N N
25 CAI H8 C H sing 1.08 N N
26 CAE H9 C H sing 1.08 N N
27 CAF H10 C H sing 1.08 N N
28 CAJ H11 C H sing 1.08 N N



0OM : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
0OM 4eh5 Open in New Window Bound ligand 1 1