Chemical Components in the PDB

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Z5J : Summary

Code

Z5J

One-letter code

X

Molecule name

beta-L-Olivopyranose

Systematic names

ProgramVersionName
ACDLabs 12.01 2,6-dideoxy-beta-L-arabino-hexopyranose
OpenEye OEToolkits 1.7.6 (4S,5R,6S)-6-methyloxane-2,4,5-triol

Formula

C6 H12 O4

Formal charge

0

Molecular weight

148.157 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 OC1C(OC(O)CC1O)C
SMILES CACTVS 3.370 C[CH]1O[CH](O)C[CH](O)[CH]1O
SMILES OpenEye OEToolkits 1.7.6 CC1C(C(CC(O1)O)O)O
Canonical SMILES CACTVS 3.370 C[C@@H]1O[C@H](O)C[C@H](O)[C@H]1O
Canonical SMILES OpenEye OEToolkits 1.7.6 C[C@H]1[C@@H]([C@H](CC(O1)O)O)O

IUPAC InChI

InChI=1S/C6H12O4/c1-3-6(9)4(7)2-5(8)10-3/h3-9H,2H2,1H3/t3-,4-,5-,6-/m0/s1

IUPAC InChI key

FDWRIIDFYSUTDP-BXKVDMCESA-N
Z5J

wwPDB Information

Atom count

22 (10 without Hydrogen)

Polymer type

Saccharide

Type description

L-saccharide, beta 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



Z5J : Atoms of Molecule

Total Number of Atoms: 22
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O4 O O1 N N N 0 2.478 -0.322 0.242
2 C4 C C1 R N N 0 1.142 -0.14 -0.229
3 C5 C C2 S N N 0 0.257 -1.277 0.289
4 C6 C C3 N N N 0 0.76 -2.609 -0.268
5 O5 O O2 N N N 0 -1.091 -1.061 -0.135
6 C3 C C4 S N N 0 0.596 1.196 0.284
7 O3 O O3 N N N 0 1.372 2.268 -0.254
8 C2 C C5 N N N 0 -0.862 1.345 -0.162
9 C1 C C6 S N N 0 -1.67 0.151 0.354
10 O1 O O4 N N Y 0 -3.019 0.254 -0.106
11 HO1 H H4O N N Y 0 -3.589 -0.472 0.183
12 H4 H H11 N N N 0 1.136 -0.142 -1.319
13 H5 H H21 N N N 0 0.296 -1.3 1.378
14 H61 H H31 N N N 0 1.788 -2.773 0.055
15 H62 H H32 N N N 0 0.13 -3.419 0.101
16 H63 H H33 N N N 0 0.721 -2.586 -1.357
17 H3 H H41 N N N 0 0.649 1.218 1.373
18 HO3 H H3O N N Y 0 1.081 3.146 0.03
19 H21 H H51 N N N 0 -1.276 2.267 0.246
20 H22 H H52 N N N 0 -0.909 1.373 -1.25
21 H1 H H61 N N N 0 -1.656 0.146 1.444
22 HO4 H H1O N N Y 0 3.095 0.363 -0.049



Z5J : Chemical Bonds

Total Number of Bonds: 22
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 C4 C5 C C sing 1.53 N N
3 C4 C3 C C sing 1.53 N N
4 C4 H4 C H sing 1.09 N N
5 C5 C6 C C sing 1.53 N N
6 C5 O5 C O sing 1.43 N N
7 C5 H5 C H sing 1.09 N N
8 C6 H61 C H sing 1.09 N N
9 C6 H62 C H sing 1.09 N N
10 C6 H63 C H sing 1.09 N N
11 O5 C1 O C sing 1.43 N N
12 C3 O3 C O sing 1.43 N N
13 C3 C2 C C sing 1.53 N N
14 C3 H3 C H sing 1.09 N N
15 O3 HO3 O H sing 0.97 N N
16 C2 C1 C C sing 1.53 N N
17 C2 H21 C H sing 1.09 N N
18 C2 H22 C H sing 1.09 N N
19 C1 O1 C O sing 1.43 N N
20 C1 H1 C H sing 1.09 N N
21 HO1 O1 H O sing 0.97 N N
22 O4 HO4 O H sing 0.97 N N



Z5J : Used in PDB Entries

Total Number of PDB Entries: 0
Ligand Code PDB Entry ID Type Total Distinct