Chemical Components in the PDB

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B55 : Summary

Code

B55

One-letter code

X

Molecule name

2-amino-8-sulfanyl-1,9-dihydro-6H-purin-6-one

Systematic names

ProgramVersionName
ACDLabs 10.04 2-amino-8-sulfanyl-1,9-dihydro-6H-purin-6-one
OpenEye OEToolkits 1.5.0 2-amino-8-sulfanyl-1,9-dihydropurin-6-one

Formula

C5 H5 N5 O S

Formal charge

0

Molecular weight

183.191 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1c2nc(S)nc2N=C(N1)N
SMILES CACTVS 3.341 NC1=Nc2[nH]c(S)nc2C(=O)N1
SMILES OpenEye OEToolkits 1.5.0 c12c([nH]c(n1)S)N=C(NC2=O)N
Canonical SMILES CACTVS 3.341 NC1=Nc2[nH]c(S)nc2C(=O)N1
Canonical SMILES OpenEye OEToolkits 1.5.0 c12c([nH]c(n1)S)N=C(NC2=O)N

IUPAC InChI

InChI=1S/C5H5N5OS/c6-4-8-2-1(3(11)10-4)7-5(12)9-2/h(H5,6,7,8,9,10,11,12)

IUPAC InChI key

JHEKNTQSGTVPAO-UHFFFAOYSA-N
B55

wwPDB Information

Atom count

17 (12 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2009-04-24

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



B55 : Atoms of Molecule

Total Number of Atoms: 17
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O1 O O1 N N N 0 -1.266 -2.553 -0.001
2 C5 C C5 N N N 0 -1.277 -1.334 0.001
3 C2 C C2 N Y N 0 -0.07 -0.6 0.008
4 N1 N N1 N Y N 0 1.245 -0.945 0.013
5 N4 N N4 N N N 0 -2.443 -0.652 -0.008
6 C4 C C4 N N N 0 -2.444 0.711 -0.006
7 N3 N N3 N N N 0 -3.644 1.378 -0.016
8 N2 N N2 N N N 0 -1.327 1.405 0.006
9 C3 C C3 N Y N 0 -0.135 0.797 0.011
10 N5 N N5 N Y N 0 1.163 1.243 0.018
11 C1 C C1 N Y N 0 1.976 0.141 0.019
12 S1 S S1 N N N 0 3.738 0.179 0.026
13 HN4 H HN4 N N N 0 -3.285 -1.135 -0.017
14 HN3 H HN3 N N N 0 -4.476 0.88 -0.024
15 HN3A H HN3A N N N 0 -3.66 2.348 -0.014
16 HN5 H HN5 N N N 0 1.452 2.169 0.02
17 HS1 H HS1 N N N 0 3.989 0.188 -1.361



B55 : Chemical Bonds

Total Number of Bonds: 18
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O1 C5 O C doub 1.22 N N
2 C5 C2 C C sing 1.41 N N
3 C5 N4 C N sing 1.35 N N
4 C2 N1 C N sing 1.36 N Y
5 C2 C3 C C doub 1.4 N Y
6 N1 C1 N C doub 1.31 N Y
7 N4 C4 N C sing 1.36 N N
8 C4 N3 C N sing 1.37 N N
9 C4 N2 C N doub 1.32 N N
10 N2 C3 N C sing 1.34 N N
11 C3 N5 C N sing 1.37 N Y
12 N5 C1 N C sing 1.37 N Y
13 C1 S1 C S sing 1.76 N N
14 N4 HN4 N H sing 0.97 N N
15 N3 HN3 N H sing 0.97 N N
16 N3 HN3A N H sing 0.97 N N
17 N5 HN5 N H sing 0.97 N N
18 S1 HS1 S H sing 1.41 N N



B55 : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
B55 3h24 Open in New Window Bound ligand 2 1
B55 3qbc Open in New Window Bound ligand 2 1