Chemical Components in the PDB

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8GA : Summary

Code

8GA

One-letter code

X

Molecule name

5-Se-methyl-5-seleno-alpha-D-ribofuranose

Synonyms

5-Se-methyl-5-seleno-alpha-D-ribose
5-Se-methyl-5-seleno-D-ribose
5-Se-methyl-5-seleno-ribose

Systematic names

ProgramVersionName
ACDLabs 12.01 5-Se-methyl-5-seleno-alpha-D-ribofuranose
OpenEye OEToolkits 2.0.6 (2~{S},3~{R},4~{S},5~{S})-5-(methylselanylmethyl)oxolane-2,3,4-triol

Formula

C6 H12 O4 Se

Formal charge

0

Molecular weight

227.117 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C[Se]CC1OC(O)C(O)C1O
SMILES CACTVS 3.385 C[Se]C[CH]1O[CH](O)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 2.0.6 C[Se]CC1C(C(C(O1)O)O)O
Canonical SMILES CACTVS 3.385 C[Se]C[C@H]1O[C@H](O)[C@H](O)[C@@H]1O
Canonical SMILES OpenEye OEToolkits 2.0.6 C[Se]C[C@@H]1[C@H]([C@H]([C@H](O1)O)O)O

IUPAC InChI

InChI=1S/C6H12O4Se/c1-11-2-3-4(7)5(8)6(9)10-3/h3-9H,2H2,1H3/t3-,4-,5-,6+/m1/s1

IUPAC InChI key

UFNQFLPLDXICBS-KAZBKCHUSA-N
8GA

wwPDB Information

Atom count

23 (11 without Hydrogen)

Polymer type

Saccharide

Type description

D-saccharide, alpha linking

Type code

ATOMS

Is modified

No

Standard parent

Not Assigned

Defined at

2017-02-04

Last modified at

2020-07-17

Status

Released

Obsoleted

Not Assigned



8GA : 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 CS C CS N N N 0 3.79 0.269 0.803
2 C5 C C5' N N N 0 0.802 0.689 0.598
3 C4 C C4' S N N 0 -0.511 0.426 -0.143
4 O4 O O4' N N N 0 -0.853 -0.961 -0.048
5 C1 C C1' S N N 0 -2.1 -1.113 0.649
6 O1 O O1' N N Y 0 -2.859 -2.183 0.081
7 C2 C C2' R N N 0 -2.839 0.234 0.452
8 O2 O O2' N N N 0 -3.492 0.283 -0.818
9 C3 C C3' S N N 0 -1.652 1.234 0.512
10 O3 O O3' N N N 0 -1.941 2.412 -0.244
11 SE SE SE N N N 0 2.268 -0.224 -0.329
12 H1A H H1 N N N 0 3.895 1.354 0.82
13 H2A H H2 N N N 0 3.622 -0.095 1.817
14 H3A H H3 N N N 0 4.701 -0.177 0.403
15 H51 H H4 N N N 0 0.998 1.761 0.62
16 H52 H H5 N N N 0 0.726 0.312 1.617
17 H4 H H6 N N N 0 -0.408 0.711 -1.19
18 H1 H H7 N N N 0 -1.921 -1.297 1.708
19 HO1 H H8 N N Y 0 -2.424 -3.045 0.136
20 H2 H H9 N N N 0 -3.547 0.416 1.262
21 HO2 H H10 N N Y 0 -4.169 -0.396 -0.939
22 H3 H H11 N N N 0 -1.407 1.484 1.544
23 HO3 H H12 N N Y 0 -2.707 2.907 0.077



8GA : Chemical Bonds

Total Number of Bonds: 23
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O3 C3 O C sing 1.43 N N
2 C3 C2 C C sing 1.55 N N
3 C3 C4 C C sing 1.54 N N
4 O2 C2 O C sing 1.43 N N
5 C2 C1 C C sing 1.55 N N
6 C5 C4 C C sing 1.53 N N
7 C5 SE C SE sing 1.96 N N
8 C4 O4 C O sing 1.43 N N
9 CS SE C SE sing 1.96 N N
10 C1 O4 C O sing 1.44 N N
11 C1 O1 C O sing 1.43 N N
12 CS H1A C H sing 1.09 N N
13 CS H2A C H sing 1.09 N N
14 CS H3A C H sing 1.09 N N
15 C5 H51 C H sing 1.09 N N
16 C5 H52 C H sing 1.09 N N
17 C4 H4 C H sing 1.09 N N
18 C1 H1 C H sing 1.09 N N
19 O1 HO1 O H sing 0.97 N N
20 C2 H2 C H sing 1.09 N N
21 O2 HO2 O H sing 0.97 N N
22 C3 H3 C H sing 1.09 N N
23 O3 HO3 O H sing 0.97 N N



8GA : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
8GA 5ulb Open in New Window Bound ligand 1 1