Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

Z61 : Summary

Code

Z61

One-letter code

X

Molecule name

2-deoxy-alpha-D-arabino-hexopyranose

Synonyms

2-deoxy-alpha-D-glucopyranose
2-deoxy-alpha-D-mannopyranose

Systematic names

ProgramVersionName
ACDLabs 12.01 2-deoxy-alpha-D-arabino-hexopyranose
OpenEye OEToolkits 1.7.6 (2S,4R,5S,6R)-6-(hydroxymethyl)oxane-2,4,5-triol

Formula

C6 H12 O5

Formal charge

0

Molecular weight

164.156 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 OC1C(OC(O)CC1O)CO
SMILES CACTVS 3.370 OC[CH]1O[CH](O)C[CH](O)[CH]1O
SMILES OpenEye OEToolkits 1.7.6 C1C(C(C(OC1O)CO)O)O
Canonical SMILES CACTVS 3.370 OC[C@H]1O[C@H](O)C[C@@H](O)[C@@H]1O
Canonical SMILES OpenEye OEToolkits 1.7.6 C1[C@H]([C@@H]([C@H](O[C@@H]1O)CO)O)O

IUPAC InChI

InChI=1S/C6H12O5/c7-2-4-6(10)3(8)1-5(9)11-4/h3-10H,1-2H2/t3-,4-,5+,6+/m1/s1

IUPAC InChI key

PMMURAAUARKVCB-ZXXMMSQZSA-N
Z61

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

2012-12-18

Last modified at

2020-07-17

Status

Released

Obsoleted

Not Assigned



Z61 : 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 O4 O O4 N N N 0 0.233 2.255 0.588
2 C1 C C1 S N N 0 0.386 -1.822 -0.304
3 C2 C C2 N N N 0 1.645 -1.009 -0.618
4 C3 C C3 R N N 0 1.602 0.306 0.167
5 C4 C C4 S N N 0 0.318 1.061 -0.192
6 C5 C C5 R N N 0 -0.889 0.168 0.105
7 C6 C C6 N N N 0 -2.173 0.892 -0.307
8 O1 O O1 N N Y 0 0.363 -2.148 1.087
9 O3 O O3 N N N 0 2.737 1.104 -0.176
10 O5 O O5 N N N 0 -0.772 -1.051 -0.632
11 O6 O O6 N N N 0 -3.305 0.109 0.076
12 H1 H H1 N N N 0 0.39 -2.74 -0.892
13 H21 H H21 N N N 0 2.527 -1.578 -0.327
14 H22 H H22 N N N 0 1.683 -0.795 -1.686
15 H3 H H3 N N N 0 1.613 0.093 1.236
16 H4 H H4 N N N 0 0.331 1.318 -1.251
17 H5 H H5 N N N 0 -0.923 -0.054 1.171
18 H61 H H61 N N N 0 -2.217 1.862 0.188
19 H62 H H62 N N N 0 -2.178 1.035 -1.388
20 HO1 H HO1 N N Y 0 -0.409 -2.664 1.357
21 HO3 H HO3 N N Y 0 3.586 0.684 0.018
22 HO6 H HO6 N N Y 0 -4.155 0.508 -0.154
23 HO4 H HO4 N N Y 0 0.97 2.866 0.454



Z61 : 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 O4 C4 O C sing 1.43 N N
2 C1 C2 C C sing 1.53 N N
3 C1 O1 C O sing 1.43 N N
4 C1 O5 C O sing 1.43 N N
5 C1 H1 C H sing 1.09 N N
6 C2 C3 C C sing 1.53 N N
7 C2 H21 C H sing 1.09 N N
8 C2 H22 C H sing 1.09 N N
9 C3 C4 C C sing 1.53 N N
10 C3 O3 C O sing 1.43 N N
11 C3 H3 C H sing 1.09 N N
12 C4 C5 C C sing 1.53 N N
13 C4 H4 C H sing 1.09 N N
14 C5 C6 C C sing 1.53 N N
15 C5 O5 C O sing 1.43 N N
16 C5 H5 C H sing 1.09 N N
17 C6 O6 C O sing 1.43 N N
18 C6 H61 C H sing 1.09 N N
19 C6 H62 C H sing 1.09 N N
20 O1 HO1 O H sing 0.97 N N
21 O3 HO3 O H sing 0.97 N N
22 O6 HO6 O H sing 0.97 N N
23 O4 HO4 O H sing 0.97 N N



Z61 : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
Z61 5hjo Open in New Window s 2 1
Z61 6x95 Open in New Window Bound ligand 1 1
Z61 7prt Open in New Window s 1 1