Chemical Components in the PDB

pdbe.org/chem
spacer

8HX : Summary

Code

8HX

One-letter code

X

Molecule name

8-hydroxy-3,9-dihydro-1H-purine-2,6-dione

Synonyms

8-hydroxyxanthine

Systematic names

ProgramVersionName
ACDLabs 12.01 8-hydroxy-3,9-dihydro-1H-purine-2,6-dione
OpenEye OEToolkits 1.7.6 8-oxidanyl-3,9-dihydropurine-2,6-dione

Formula

C5 H4 N4 O3

Formal charge

0

Molecular weight

168.11 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C2c1nc(O)nc1NC(=O)N2
SMILES CACTVS 3.385 Oc1[nH]c2NC(=O)NC(=O)c2n1
SMILES OpenEye OEToolkits 1.7.6 c12c([nH]c(n1)O)NC(=O)NC2=O
Canonical SMILES CACTVS 3.385 Oc1[nH]c2NC(=O)NC(=O)c2n1
Canonical SMILES OpenEye OEToolkits 1.7.6 c12c([nH]c(n1)O)NC(=O)NC2=O

IUPAC InChI

InChI=1S/C5H4N4O3/c10-3-1-2(7-4(11)6-1)8-5(12)9-3/h(H4,6,7,8,9,10,11,12)

IUPAC InChI key

LEHOTFFKMJEONL-UHFFFAOYSA-N
8HX

wwPDB Information

Atom count

16 (12 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-10-29

Last modified at

2014-01-31

Status

Released

Obsoleted

Not Assigned



8HX : Atoms of Molecule

Total Number of Atoms: 16
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N N N 0 2.07 0.65 -0.0080
2 C2 C C2 N N N 0 2.087 -0.693 -0.0060
3 O2 O O2 N N N 0 3.159 -1.268 -0.01
4 N3 N N3 N N N 0 0.958 -1.425 0.0020
5 C4 C C4 N Y N 0 -0.276 -0.815 0.0070
6 C5 C C5 N Y N 0 -0.347 0.571 0.0050
7 C6 C C6 N N N 0 0.903 1.33 0.0020
8 O6 O O6 N N N 0 0.892 2.547 0.0
9 N7 N N7 N Y N 0 -1.662 0.912 0.012
10 C8 C C8 N Y N 0 -2.384 -0.177 0.018
11 O8 O O8 N N N 0 -3.738 -0.218 0.025
12 N9 N N9 N Y N 0 -1.561 -1.269 0.015
13 HAC H HAC N N N 0 2.908 1.139 -0.013
14 H1 H H1 N N N 0 1.015 -2.393 0.0030
15 HAA H HAA N N N 0 -4.136 -0.231 -0.856
16 HAB H HAB N N N 0 -1.841 -2.197 0.019



8HX : Chemical Bonds

Total Number of Bonds: 17
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O6 C6 O C doub 1.2170514 N N
2 C6 N1 C N sing 1.3506994 N N
3 C6 C5 C C sing 1.4623919 N N
4 N1 C2 N C sing 1.3431091 N N
5 C5 N7 C N sing 1.358512 N Y
6 C5 C4 C C doub 1.3878188 N Y
7 N7 C8 N C doub 1.3066143 N Y
8 C2 O2 C O doub 1.2164806 N N
9 C2 N3 C N sing 1.345559 N N
10 C4 N3 C N sing 1.3765467 N N
11 C4 N9 C N sing 1.3628665 N Y
12 C8 O8 C O sing 1.3546387 N N
13 C8 N9 C N sing 1.3674071 N Y
14 N1 HAC N H sing 0.9702526 N N
15 N3 H1 N H sing 0.96967727 N N
16 O8 HAA O H sing 0.9668164 N N
17 N9 HAB N H sing 0.96932966 N N



8HX : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
8HX 4n9m Open in New Window Bound ligand 1 1
8HX 4n9s Open in New Window Bound ligand 1 1