Chemical Components in the PDB

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

LDY : Summary

Code

LDY

One-letter code

X

Molecule name

alpha-D-lyxopyranose

Systematic names

ProgramVersionName
ACDLabs 10.04 alpha-D-lyxopyranose
OpenEye OEToolkits 1.5.0 (2S,3S,4S,5R)-oxane-2,3,4,5-tetrol

Formula

C5 H10 O5

Formal charge

0

Molecular weight

150.13 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 OC1C(O)COC(O)C1O
SMILES CACTVS 3.341 O[CH]1CO[CH](O)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 1.5.0 C1C(C(C(C(O1)O)O)O)O
Canonical SMILES CACTVS 3.341 O[C@@H]1CO[C@H](O)[C@@H](O)[C@H]1O
Canonical SMILES OpenEye OEToolkits 1.5.0 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+/m1/s1

IUPAC InChI key

SRBFZHDQGSBBOR-STGXQOJASA-N
LDY

wwPDB Information

Atom count

20 (10 without Hydrogen)

Polymer type

Saccharide

Type description

D-SACCHARIDE

Type code

ATOMS

Is modified

No

Standard parent

Not Assigned

Defined at

2008-01-09

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



LDY : 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 C5 C C5 N N N 0 1.232 -1.065 0.872
2 O5 O O5 N N N 0 -0.012 -1.579 0.391
3 C1 C C1 S N N 0 -1.067 -0.615 0.358
4 C2 C C2 S N N 0 -0.682 0.527 -0.586
5 O2 O O2 N N N 0 -1.71 1.52 -0.578
6 C3 C C3 S N N 0 0.635 1.15 -0.112
7 O3 O O3 N N N 0 0.456 1.717 1.187
8 C4 C C4 R N N 0 1.709 0.059 -0.052
9 O4 O O4 N N N 0 1.934 -0.462 -1.363
10 O1 O O1 N N Y 0 -2.265 -1.237 -0.11
11 H5 H H5 N N N 0 1.099 -0.675 1.881
12 H5A H H5A N N N 0 1.974 -1.864 0.885
13 H1 H H1 N N N 0 -1.23 -0.219 1.36
14 H2 H H2 N N N 0 -0.559 0.139 -1.597
15 HO2 H HO2 N N N 0 -2.575 1.193 -0.864
16 H3 H H3 N N N 0 0.943 1.927 -0.811
17 HO3 H HO3 N N N 0 1.252 2.129 1.55
18 H4 H H4 N N N 0 2.635 0.482 0.338
19 HO4 H HO4 N N N 0 2.605 -1.159 -1.399
20 HO1 H HO1 N N N 0 -2.568 -1.972 0.441



LDY : 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 C4 C5 C C sing 1.53 N N
2 C5 O5 C O sing 1.43 N N
3 C5 H5 C H sing 1.09 N N
4 C5 H5A C H sing 1.09 N N
5 C1 O5 C O sing 1.43 N N
6 C2 C1 C C sing 1.53 N N
7 C1 O1 C O sing 1.43 N N
8 C1 H1 C H sing 1.09 N N
9 O2 C2 O C sing 1.43 N N
10 C3 C2 C C sing 1.53 N N
11 C2 H2 C H sing 1.09 N N
12 O2 HO2 O H sing 0.97 N N
13 O3 C3 O C sing 1.43 N N
14 C3 C4 C C sing 1.53 N N
15 C3 H3 C H sing 1.09 N N
16 O3 HO3 O H sing 0.97 N N
17 C4 O4 C O sing 1.43 N N
18 C4 H4 C H sing 1.09 N N
19 O4 HO4 O H sing 0.97 N N
20 O1 HO1 O H sing 0.97 N N



LDY : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
LDY 2ri9 Open in New Window Bound ligand 2 1