Chemical Components in the PDB

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8HG : Summary

Code

8HG

One-letter code

X

Molecule name

2'-DEOXY-8-OXOGUANOSINE

Systematic names

ProgramVersionName
ACDLabs 10.04 2'-deoxy-8-oxoguanosine
OpenEye OEToolkits 1.5.0 2-amino-9-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,7-dihydropurine-6,8-dione

Formula

C10 H13 N5 O5

Formal charge

0

Molecular weight

283.241 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1C=2NC(=O)N(C=2N=C(N)N1)C3OC(C(O)C3)CO
SMILES CACTVS 3.341 NC1=NC2=C(NC(=O)N2[CH]3C[CH](O)[CH](CO)O3)C(=O)N1
SMILES OpenEye OEToolkits 1.5.0 C1C(C(OC1N2C3=C(C(=O)NC(=N3)N)NC2=O)CO)O
Canonical SMILES CACTVS 3.341 NC1=NC2=C(NC(=O)N2[C@H]3C[C@H](O)[C@@H](CO)O3)C(=O)N1
Canonical SMILES OpenEye OEToolkits 1.5.0 C1[C@@H]([C@H](O[C@H]1N2C3=C(C(=O)NC(=N3)N)NC2=O)CO)O

IUPAC InChI

InChI=1S/C10H13N5O5/c11-9-13-7-6(8(18)14-9)12-10(19)15(7)5-1-3(17)4(2-16)20-5/h3-5,16-17H,1-2H2,(H,12,19)(H3,11,13,14,18)/t3-,4+,5+/m0/s1

IUPAC InChI key

HCAJQHYUCKICQH-VPENINKCSA-N
8HG

wwPDB Information

Atom count

33 (20 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2004-10-21

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



8HG : 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' R N N 0 -1.072 0.514 -0.172
2 C2 C C2 N N N 0 3.233 1.597 0.321
3 C2' C C2' N N N 0 -1.788 0.404 -1.536
4 C3' C C3' S N N 0 -3.29 0.401 -1.172
5 C4 C C4 N N N 0 1.432 0.186 -0.004
6 C4' C C4' R N N 0 -3.303 0.508 0.368
7 C5 C C5 N N N 0 2.287 -0.906 -0.074
8 C5' C C5' N N N 0 -4.434 -0.342 0.952
9 C6 C C6 N N N 0 3.667 -0.701 0.072
10 C8 C C8 N N N 0 0.207 -1.628 -0.347
11 H1 H H1 N N N 0 -3.919 1.539 -2.725
12 H1' H H1' N N N 0 -0.838 1.554 0.054
13 H2'1 H H2'1 N N N 0 -1.549 1.263 -2.163
14 H2'2 H H2'2 N N N 0 -1.514 -0.524 -2.038
15 H3' H H3' N N N 0 -3.759 -0.528 -1.497
16 H4' H H4' N N N 0 -3.413 1.548 0.675
17 H5' H H5' N N N 0 -5.149 -0.707 2.811
18 H5'1 H H5'1 N N N 0 -5.387 -0.013 0.538
19 H5'2 H H5'2 N N N 0 -4.269 -1.389 0.697
20 HN1 H HN1 N N N 0 5.064 0.726 0.365
21 HN21 H HN21 N N N 0 4.662 3.02 0.616
22 HN22 H HN22 N N N 0 3.092 3.615 0.56
23 N1 N N1 N N N 0 4.114 0.56 0.265
24 N2 N N2 N N N 0 3.709 2.868 0.518
25 N3 N N3 N N N 0 1.938 1.41 0.191
26 N7 N N7 N N N 0 1.491 -2.034 -0.287
27 O20 O O20 N N N 0 -0.752 -2.356 -0.522
28 O3' O O3' N N N 0 -3.95 1.524 -1.759
29 O4' O O4' N N N 0 -2.02 -0.007 0.786
30 O5' O O5' N N N 0 -4.455 -0.195 2.373
31 O6 O O6 N N N 0 4.447 -1.638 0.019
32 N9 N N9 N N N 0 0.15 -0.295 -0.17
33 H13 H H13 N N N 0 1.806 -2.947 -0.376



8HG : Chemical Bonds

Total Number of Bonds: 35
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O6 C6 O C doub 1.22 N N
2 C6 N1 C N sing 1.35 N N
3 C6 C5 C C sing 1.4 N N
4 N1 C2 N C sing 1.36 N N
5 N1 HN1 N H sing 0.97 N N
6 C2 N2 C N sing 1.37 N N
7 C2 N3 C N doub 1.31 N N
8 N2 HN21 N H sing 0.97 N N
9 N2 HN22 N H sing 0.97 N N
10 N3 C4 N C sing 1.34 N N
11 C4 C5 C C doub 1.39 N N
12 C4 N9 C N sing 1.38 N N
13 C5 N7 C N sing 1.4 N N
14 N7 C8 N C sing 1.35 N N
15 C8 O20 C O doub 1.22 N N
16 C8 N9 C N sing 1.35 N N
17 N9 C1' N C sing 1.47 N N
18 C1' O4' C O sing 1.44 N N
19 C1' C2' C C sing 1.54 N N
20 C1' H1' C H sing 1.09 N N
21 O4' C4' O C sing 1.44 N N
22 C2' C3' C C sing 1.55 N N
23 C2' H2'1 C H sing 1.09 N N
24 C2' H2'2 C H sing 1.09 N N
25 C3' O3' C O sing 1.43 N N
26 C3' C4' C C sing 1.54 N N
27 C3' H3' C H sing 1.09 N N
28 O3' H1 O H sing 0.97 N N
29 C4' C5' C C sing 1.53 N N
30 C4' H4' C H sing 1.09 N N
31 C5' O5' C O sing 1.43 N N
32 C5' H5'1 C H sing 1.09 N N
33 C5' H5'2 C H sing 1.09 N N
34 O5' H5' O H sing 0.97 N N
35 N7 H13 N H sing 0.97 N N



8HG : Used in PDB Entries

Total Number of PDB Entries: 4
Ligand Code PDB Entry ID Type Total Distinct
8HG 1xqp Open in New Window Bound ligand 2 1
8HG 2a5b Open in New Window Bound ligand 1 1
8HG 3f10 Open in New Window Bound ligand 1 1
8HG 7oli Open in New Window Bound ligand 2 1