Chemical Components in the PDB

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

LXC : Summary

Code

LXC

One-letter code

X

Molecule name

BETA-L-XYLOPYRANOSE

Synonyms

L-XYLOSE (CYCLIC FORM)

Systematic names

ProgramVersionName
ACDLabs 10.04 beta-L-xylopyranose
OpenEye OEToolkits 1.5.0 (2S,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 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-/m0/s1

IUPAC InChI key

SRBFZHDQGSBBOR-QTBDOELSSA-N
LXC

wwPDB Information

Atom count

20 (10 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

ATOMS

Is modified

No

Standard parent

Not Assigned

Defined at

2002-03-13

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



LXC : 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 S N N 0 0.509 -0.253 -1.37
2 C2 C C2 S N N 0 -0.78 0.228 -0.701
3 C3 C C3 R N N 0 -0.779 -0.213 0.766
4 C4 C C4 S N N 0 0.519 0.269 1.423
5 C5 C C5 N N N 0 1.71 -0.215 0.593
6 H1 H H1 N N N 0 0.571 -1.338 -1.297
7 H2 H H2 N N N 0 -0.833 1.316 -0.752
8 H3 H H3 N N N 0 -0.831 -1.301 0.82
9 H4 H H4 N N N 0 0.523 1.358 1.465
10 H5C1 H 1H5C N N N 0 2.637 0.105 1.068
11 H5C2 H 2H5C N N N 0 1.691 -1.304 0.535
12 HA H HA N N N 0 1.325 -0.194 -3.132
13 HB H HB N N N 0 -1.865 -0.037 -2.291
14 HC H HC N N N 0 -1.864 0.051 2.356
15 HD H HD N N N 0 1.441 0.064 3.121
16 O1 O O1 N N Y 0 0.501 0.13 -2.746
17 O2 O O2 N N N 0 -1.907 -0.337 -1.372
18 O3 O O3 N N N 0 -1.904 0.354 1.439
19 O4 O O4 N N N 0 0.611 -0.26 2.747
20 O5 O O5 N N N 0 1.637 0.331 -0.721



LXC : 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 O5 C O sing 1.42 N N
2 C5 C4 C C sing 1.53 N N
3 C5 H5C1 C H sing 1.09 N N
4 C5 H5C2 C H sing 1.09 N N
5 O5 C1 O C sing 1.43 N N
6 C1 O1 C O sing 1.43 N N
7 C1 C2 C C sing 1.53 N N
8 C1 H1 C H sing 1.09 N N
9 O1 HA O H sing 0.97 N N
10 C2 O2 C O sing 1.43 N N
11 C2 C3 C C sing 1.53 N N
12 C2 H2 C H sing 1.09 N N
13 O2 HB O H sing 0.97 N N
14 C3 O3 C O sing 1.43 N N
15 C3 C4 C C sing 1.53 N N
16 C3 H3 C H sing 1.09 N N
17 O3 HC O H sing 0.97 N N
18 C4 O4 C O sing 1.43 N N
19 C4 H4 C H sing 1.09 N N
20 O4 HD O H sing 0.97 N N



LXC : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
LXC 1gw9 Open in New Window Bound ligand 2 1
LXC 2dsf Open in New Window Bound ligand 1 1
LXC 2fgl Open in New Window Bound ligand 1 1