Chemical Components in the PDB

pdbe.org/chem
spacer

1OX : Summary

Code

1OX

One-letter code

X

Molecule name

2-(1H-benzimidazol-1-ylmethyl)-4H-pyrido[1,2-a]pyrimidin-4-one

Systematic names

ProgramVersionName
ACDLabs 12.01 2-(1H-benzimidazol-1-ylmethyl)-4H-pyrido[1,2-a]pyrimidin-4-one
OpenEye OEToolkits 1.7.6 2-(benzimidazol-1-ylmethyl)pyrido[1,2-a]pyrimidin-4-one

Formula

C16 H12 N4 O

Formal charge

0

Molecular weight

276.293 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C2C=C(N=C1C=CC=CN12)Cn3c4ccccc4nc3
SMILES CACTVS 3.370 O=C1C=C(Cn2cnc3ccccc23)N=C4C=CC=CN14
SMILES OpenEye OEToolkits 1.7.6 c1ccc2c(c1)ncn2CC3=CC(=O)N4C=CC=CC4=N3
Canonical SMILES CACTVS 3.370 O=C1C=C(Cn2cnc3ccccc23)N=C4C=CC=CN14
Canonical SMILES OpenEye OEToolkits 1.7.6 c1ccc2c(c1)ncn2CC3=CC(=O)N4C=CC=CC4=N3

IUPAC InChI

InChI=1S/C16H12N4O/c21-16-9-12(18-15-7-3-4-8-20(15)16)10-19-11-17-13-5-1-2-6-14(13)19/h1-9,11H,10H2

IUPAC InChI key

BCWFSHAZZLFCIE-UHFFFAOYSA-N
1OX

wwPDB Information

Atom count

33 (21 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-04-16

Last modified at

2013-05-17

Status

Released

Obsoleted

Not Assigned



1OX : Atoms of Molecule

Total Number of Atoms: 33
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N Y N 0 4.257 1.97 -0.645
2 C10 C C10 N N N 0 -4.411 1.561 -0.751
3 C11 C C11 N N N 0 -1.352 -1.872 0.348
4 C12 C C12 N N N 0 -4.063 0.254 -0.76
5 C13 C C13 N N N 0 -0.536 -0.921 0.929
6 C14 C C14 N N N 0 -2.045 0.746 0.379
7 C15 C C15 N N N 0 -2.566 -1.468 -0.219
8 C16 C C16 N N N 0 0.777 -1.331 1.545
9 C2 C C2 N Y N 0 3.341 2.274 0.351
10 C3 C C3 N Y N 0 4.328 0.708 -1.166
11 C4 C C4 N Y N 0 2.485 1.305 0.833
12 C5 C C5 N Y N 0 2.366 -2.108 -0.253
13 C6 C C6 N Y N 0 3.476 -0.29 -0.689
14 C7 C C7 N Y N 0 2.543 0.018 0.316
15 C8 C C8 N N N 0 -3.566 2.511 -0.162
16 C9 C C9 N N N 0 -2.393 2.109 0.402
17 H1 H H1 N N N 0 4.918 2.739 -1.016
18 H11 H H11 N N N 0 -4.721 -0.471 -1.216
19 H12 H H12 N N N 0 0.975 -0.714 2.421
20 H13 H H13 N N N 0 0.728 -2.378 1.842
21 H2 H H2 N N N 0 3.297 3.275 0.752
22 H3 H H3 N N N 0 5.042 0.484 -1.944
23 H4 H H4 N N N 0 1.771 1.548 1.606
24 H5 H H5 N N N 0 2.031 -3.134 -0.292
25 H6 H H6 N N N 0 -3.845 3.555 -0.151
26 H7 H H7 N N N 0 -1.735 2.831 0.863
27 H8 H H8 N N N 0 -5.343 1.873 -1.2
28 H9 H H9 N N N 0 -1.064 -2.913 0.342
29 N17 N N17 N Y N 0 3.308 -1.603 -0.994
30 N18 N N18 N N N 0 -0.899 0.352 0.93
31 N19 N N19 N Y N 0 1.853 -1.151 0.567
32 N20 N N20 N N N 0 -2.892 -0.157 -0.198
33 O21 O O21 N N N 0 -3.312 -2.284 -0.736



1OX : Chemical Bonds

Total Number of Bonds: 36
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C12 C10 C C doub 1.35 N N
2 C12 N20 C N sing 1.36 N N
3 C10 C8 C C sing 1.4 N N
4 O21 C15 O C doub 1.22 N N
5 C15 N20 C N sing 1.35 N N
6 C15 C11 C C sing 1.4 N N
7 N20 C14 N C sing 1.37 N N
8 C8 C9 C C doub 1.36 N N
9 C11 C13 C C doub 1.38 N N
10 C14 C9 C C sing 1.41 N N
11 C14 N18 C N doub 1.33 N N
12 C13 N18 C N sing 1.32 N N
13 C13 C16 C C sing 1.51 N N
14 C16 N19 C N sing 1.47 N N
15 C4 C7 C C doub 1.39 N Y
16 C4 C2 C C sing 1.38 N Y
17 N19 C7 N C sing 1.38 N Y
18 N19 C5 N C sing 1.36 N Y
19 C7 C6 C C sing 1.41 N Y
20 C2 C1 C C doub 1.39 N Y
21 C5 N17 C N doub 1.3 N Y
22 C6 N17 C N sing 1.36 N Y
23 C6 C3 C C doub 1.4 N Y
24 C1 C3 C C sing 1.37 N Y
25 C1 H1 C H sing 1.08 N N
26 C2 H2 C H sing 1.08 N N
27 C3 H3 C H sing 1.08 N N
28 C4 H4 C H sing 1.08 N N
29 C5 H5 C H sing 1.08 N N
30 C8 H6 C H sing 1.08 N N
31 C9 H7 C H sing 1.08 N N
32 C10 H8 C H sing 1.08 N N
33 C11 H9 C H sing 1.08 N N
34 C12 H11 C H sing 1.08 N N
35 C16 H12 C H sing 1.09 N N
36 C16 H13 C H sing 1.09 N N



1OX : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
1OX 4jpg Open in New Window Bound ligand 2 1