Chemical Components in the PDB

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XU1 : Summary

Code

XU1

One-letter code

X

Molecule name

benzo[c][1,8]naphthyridin-6(5H)-one

Systematic names

ProgramVersionName
ACDLabs 12.01 benzo[c][1,8]naphthyridin-6(5H)-one
OpenEye OEToolkits 1.7.6 5H-benzo[c][1,8]naphthyridin-6-one

Formula

C12 H8 N2 O

Formal charge

0

Molecular weight

196.205 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C2c3c(c1c(nccc1)N2)cccc3
SMILES CACTVS 3.370 O=C1Nc2ncccc2c3ccccc13
SMILES OpenEye OEToolkits 1.7.6 c1ccc2c(c1)-c3cccnc3NC2=O
Canonical SMILES CACTVS 3.370 O=C1Nc2ncccc2c3ccccc13
Canonical SMILES OpenEye OEToolkits 1.7.6 c1ccc2c(c1)-c3cccnc3NC2=O

IUPAC InChI

InChI=1S/C12H8N2O/c15-12-10-5-2-1-4-8(10)9-6-3-7-13-11(9)14-12/h1-7H,(H,13,14,15)

IUPAC InChI key

YLSBDRGLLZDAKB-UHFFFAOYSA-N
XU1

wwPDB Information

Atom count

23 (15 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-02-21

Last modified at

2013-05-17

Status

Released

Obsoleted

Not Assigned



XU1 : Atoms of Molecule

Total Number of Atoms: 23
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 -0.868 0.56 0.0010
2 C10 C C10 N Y N 0 3.364 0.907 0.0
3 C11 C C11 N Y N 0 2.582 2.052 0.0020
4 C12 C C12 N Y N 0 1.206 1.963 0.0010
5 C2 C C2 N Y N 0 -1.706 1.675 -0.0030
6 C3 C C3 N Y N 0 -3.075 1.464 -0.0040
7 C4 C C4 N Y N 0 -3.559 0.168 -0.0030
8 C5 C C5 N Y N 0 -1.429 -0.728 0.0020
9 C6 C C6 N N N 0 0.724 -1.764 0.0020
10 C7 C C7 N Y N 0 1.391 -0.454 0.0050
11 C8 C C8 N Y N 0 0.598 0.712 0.0030
12 C9 C C9 N Y N 0 2.78 -0.342 -0.0050
13 H1 H H1 N N N 0 3.055 3.023 0.0010
14 H2 H H2 N N N 0 0.603 2.859 -0.0010
15 H3 H H3 N N N 0 4.44 0.994 -0.0080
16 H4 H H4 N N N 0 3.396 -1.23 -0.0070
17 H5 H H5 N N N 0 -1.033 -2.724 0.01
18 H6 H H6 N N N 0 -4.627 0.0030 -0.0040
19 H7 H H7 N N N 0 -3.756 2.302 -0.0080
20 H8 H H8 N N N 0 -1.299 2.675 -0.0030
21 N1 N N1 N Y N 0 -2.748 -0.87 0.0
22 N2 N N2 N N N 0 -0.618 -1.847 0.013
23 O1 O O1 N N N 0 1.391 -2.782 -0.011



XU1 : Chemical Bonds

Total Number of Bonds: 25
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C10 C9 C C doub 1.38 N Y
2 C10 C11 C C sing 1.39 N Y
3 C9 C7 C C sing 1.39 N Y
4 C11 C12 C C doub 1.38 N Y
5 C7 C8 C C doub 1.41 N Y
6 C7 C6 C C sing 1.47 N N
7 C12 C8 C C sing 1.39 N Y
8 O1 C6 O C doub 1.22 N N
9 C8 C1 C C sing 1.47 N N
10 C6 N2 C N sing 1.34 N N
11 C1 C2 C C doub 1.39 N Y
12 C1 C5 C C sing 1.4 N Y
13 N2 C5 N C sing 1.38 N N
14 C2 C3 C C sing 1.39 N Y
15 C5 N1 C N doub 1.33 N Y
16 C3 C4 C C doub 1.38 N Y
17 N1 C4 N C sing 1.32 N Y
18 C11 H1 C H sing 1.08 N N
19 C12 H2 C H sing 1.08 N N
20 C10 H3 C H sing 1.08 N N
21 C9 H4 C H sing 1.08 N N
22 N2 H5 N H sing 0.97 N N
23 C4 H6 C H sing 1.08 N N
24 C3 H7 C H sing 1.08 N N
25 C2 H8 C H sing 1.08 N N



XU1 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
XU1 4jaj Open in New Window Bound ligand 1 1