Chemical Components in the PDB

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  • 0MK (Stereoisomer)
  • LDY (Stereoisomer)
  • XYP (Stereoisomer)
  • XYS (Stereoisomer)
  • ARA (Stereoisomer)
  • RIP (Stereoisomer)
  • LXC (Stereoisomer)
  • ARB (Stereoisomer)

HSY : Summary

Code

HSY

One-letter code

X

Molecule name

alpha-L-xylopyranose

Systematic names

ProgramVersionName
ACDLabs 12.01 alpha-L-xylopyranose
OpenEye OEToolkits 1.7.0 (2R,3S,4R,5S)-oxane-2,3,4,5-tetrol

Formula

C5 H10 O5

Formal charge

0

Molecular weight

150.13 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 OC1C(O)COC(O)C1O
SMILES CACTVS 3.370 O[CH]1CO[CH](O)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 1.7.0 C1C(C(C(C(O1)O)O)O)O
Canonical SMILES CACTVS 3.370 O[C@H]1CO[C@@H](O)[C@@H](O)[C@@H]1O
Canonical SMILES OpenEye OEToolkits 1.7.0 C1[C@@H]([C@H]([C@@H]([C@@H](O1)O)O)O)O

IUPAC InChI

InChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3+,4-,5+/m0/s1

IUPAC InChI key

SRBFZHDQGSBBOR-SKNVOMKLSA-N
HSY

wwPDB Information

Atom count

20 (10 without Hydrogen)

Polymer type

Saccharide

Type description

SACCHARIDE

Type code

ATOMS

Is modified

No

Standard parent

Not Assigned

Defined at

2009-01-16

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



HSY : Atoms of Molecule

Total Number of Atoms: 20
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 0.688 1.67 0.066
2 C2 C C2 S N N 0 1.396 0.332 0.291
3 C3 C C3 R N N 0 0.497 -0.803 -0.21
4 C4 C C4 S N N 0 -0.851 -0.73 0.514
5 C5 C C5 R N N 0 -1.472 0.65 0.281
6 H1 H H1 N N N 0 1.304 2.478 0.46
7 H10 H H10 N N Y 0 -2.114 1.686 -1.337
8 H1A H H1A N N N 0 0.527 1.822 -1.001
9 H2 H H2 N N N 0 1.593 0.198 1.355
10 H3 H H3 N N N 0 0.34 -0.698 -1.283
11 H4 H H4 N N N 0 -0.699 -0.885 1.583
12 H5 H H5 N N N 0 -2.411 0.723 0.829
13 HO2 H HO2 N N N 0 3.249 1.011 -0.163
14 HO3 H HO3 N N N 0 1.978 -2.176 -0.365
15 HO4 H HO4 N N N 0 -2.599 -1.748 0.414
16 O2 O O2 N N N 0 2.63 0.317 -0.43
17 O3 O O3 N N N 0 1.118 -2.061 0.063
18 O4 O O4 N N N 0 -1.723 -1.739 0.0030
19 O5 O O5 N N N 0 -0.572 1.66 0.74
20 O51 O O51 N N Y 0 -1.719 0.831 -1.115



HSY : Chemical Bonds

Total Number of Bonds: 20
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C5 C4 C C sing 1.5311205 N N
2 C5 O5 C O sing 1.4285591 N N
3 C5 O51 C O sing 1.4291906 N N
4 C5 H5 C H sing 1.0896578 N N
5 C4 C3 C C sing 1.5318645 N N
6 C4 O4 C O sing 1.4281408 N N
7 C4 H4 C H sing 1.0908208 N N
8 C3 C2 C C sing 1.5321316 N N
9 C3 O3 C O sing 1.4292425 N N
10 C3 H3 C H sing 1.0894967 N N
11 C2 C1 C C sing 1.5304029 N N
12 C2 O2 C O sing 1.4292732 N N
13 C2 H2 C H sing 1.0903491 N N
14 C1 O5 C O sing 1.4289773 N N
15 C1 H1 C H sing 1.0897504 N N
16 C1 H1A C H sing 1.0897312 N N
17 O4 HO4 O H sing 0.96766627 N N
18 O3 HO3 O H sing 0.9674756 N N
19 O2 HO2 O H sing 0.96751535 N N
20 O51 H10 O H sing 0.96764356 N N



HSY : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
HSY 1apw Open in New Window Bound ligand 1 1
HSY 1ppk Open in New Window Bound ligand 1 1