Chemical Components in the PDB

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AXV : Summary

Code

AXV

One-letter code

X

Molecule name

1~{H}-benzimidazol-2-ylcyanamide

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 1~{H}-benzimidazol-2-ylcyanamide

Formula

C8 H6 N4

Formal charge

0

Molecular weight

158.16 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 N#CNc1[nH]c2ccccc2n1
SMILES OpenEye OEToolkits 2.0.6 c1ccc2c(c1)[nH]c(n2)NC#N
Canonical SMILES CACTVS 3.385 N#CNc1[nH]c2ccccc2n1
Canonical SMILES OpenEye OEToolkits 2.0.6 c1ccc2c(c1)[nH]c(n2)NC#N

IUPAC InChI

InChI=1S/C8H6N4/c9-5-10-8-11-6-3-1-2-4-7(6)12-8/h1-4H,(H2,10,11,12)

IUPAC InChI key

NYLIXUBOFQIMGV-UHFFFAOYSA-N
AXV

wwPDB Information

Atom count

18 (12 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-07-28

Last modified at

2018-08-03

Status

Released

Obsoleted

Not Assigned



AXV : Atoms of Molecule

Total Number of Atoms: 18
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N Y N 0 0.617 0.726 0.004
2 N3 N N2 N N N 0 2.478 -0.849 0.0
3 C4 C C1 N Y N 0 -1.038 -0.769 -0.001
4 C5 C C2 N Y N 0 -0.763 0.609 0.002
5 C6 C C3 N Y N 0 -1.806 1.523 0.002
6 C7 C C4 N Y N 0 1.13 -0.539 0.002
7 C8 C C5 N N N 0 3.401 0.143 -0.002
8 C1 C C6 N Y N 0 -3.111 1.075 -0.001
9 C2 C C7 N Y N 0 -3.388 -0.284 -0.004
10 C3 C C8 N Y N 0 -2.365 -1.205 -0.003
11 N2 N N3 N Y N 0 0.157 -1.415 0.005
12 N4 N N4 N N N 0 4.175 0.974 -0.004
13 H1 H H1 N N N 0 1.124 1.553 0.002
14 H2 H H2 N N N 0 2.762 -1.776 -0.001
15 H3 H H3 N N N 0 -1.597 2.582 0.004
16 H4 H H4 N N N 0 -3.922 1.788 -0.001
17 H5 H H5 N N N 0 -4.414 -0.622 -0.005
18 H6 H H6 N N N 0 -2.588 -2.262 -0.005



AXV : Chemical Bonds

Total Number of Bonds: 19
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C doub 1.39 N Y
2 C1 C6 C C sing 1.38 N Y
3 C2 C3 C C sing 1.38 N Y
4 C6 C5 C C doub 1.39 N Y
5 C3 C4 C C doub 1.4 N Y
6 C5 C4 C C sing 1.41 N Y
7 C5 N1 C N sing 1.38 N Y
8 C4 N2 C N sing 1.36 N Y
9 N1 C7 N C sing 1.37 N Y
10 N2 C7 N C doub 1.31 N Y
11 C7 N3 C N sing 1.38 N N
12 N3 C8 N C sing 1.35 N N
13 C8 N4 C N trip 1.14 N N
14 N1 H1 N H sing 0.97 N N
15 N3 H2 N H sing 0.97 N N
16 C6 H3 C H sing 1.08 N N
17 C1 H4 C H sing 1.08 N N
18 C2 H5 C H sing 1.08 N N
19 C3 H6 C H sing 1.08 N N



AXV : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
AXV 5q1w Open in New Window Bound ligand 3 1
AXV 7b8k Open in New Window Bound ligand 1 1