Chemical Components in the PDB

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  • LDY (Stereoisomer)
  • LXC (Stereoisomer)
  • 64K (Stereoisomer)
  • HSY (Stereoisomer)
  • XYP (Stereoisomer)
  • XYS (Stereoisomer)
  • RIP (Stereoisomer)
  • ARB (Stereoisomer)
  • 0MK (Stereoisomer)

ARA : Summary

Code

ARA

One-letter code

X

Molecule name

ALPHA-L-ARABINOSE

Systematic names

ProgramVersionName
ACDLabs 10.04 alpha-L-arabinopyranose
OpenEye OEToolkits 1.5.0 (2R,3R,4S,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-QMKXCQHVSA-N
ARA

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

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



ARA : 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 R N N 0 0.316 -0.253 1.356
2 C2 C C2 R N N 0 -0.817 0.217 0.443
3 C3 C C3 S N N 0 -0.716 -0.517 -0.9
4 C4 C C4 S N N 0 0.697 -0.321 -1.458
5 C5 C C5 N N N 0 1.716 -0.751 -0.401
6 O1 O O1 N N Y 0 0.21 0.403 2.621
7 O2 O O2 N N N 0 -2.076 -0.073 1.055
8 O3 O O3 N N N 0 -1.677 0.018 -1.813
9 O4 O O4 N N N 0 0.896 1.056 -1.782
10 O5 O O5 N N N 0 1.575 0.058 0.764
11 H1 H H1 N N N 0 0.241 -1.331 1.501
12 H2 H H2 N N N 0 -0.731 1.291 0.278
13 H3 H H3 N N N 0 -0.907 -1.58 -0.751
14 H4 H H4 N N N 0 0.823 -0.928 -2.354
15 H51 H 1H5 N N N 0 1.548 -1.795 -0.139
16 H52 H 2H5 N N N 0 2.724 -0.637 -0.801
17 HO1 H HO1 N N N 0 0.938 0.077 3.167
18 HO2 H HO2 N N N 0 -2.094 0.402 1.896
19 HO3 H HO3 N N N 0 -1.578 -0.471 -2.641
20 HO4 H HO4 N N N 0 1.796 1.135 -2.126



ARA : 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 C1 C2 C C sing 1.53 N N
2 C1 O1 C O sing 1.43 N N
3 C1 O5 C O sing 1.43 N N
4 C1 H1 C H sing 1.09 N N
5 C2 C3 C C sing 1.53 N N
6 C2 O2 C O sing 1.43 N N
7 C2 H2 C H sing 1.09 N N
8 C3 C4 C C sing 1.53 N N
9 C3 O3 C O sing 1.43 N N
10 C3 H3 C H sing 1.09 N N
11 C4 C5 C C sing 1.53 N N
12 C4 O4 C O sing 1.43 N N
13 C4 H4 C H sing 1.09 N N
14 C5 O5 C O sing 1.43 N N
15 C5 H51 C H sing 1.09 N N
16 C5 H52 C H sing 1.09 N N
17 O1 HO1 O H sing 0.97 N N
18 O2 HO2 O H sing 0.97 N N
19 O3 HO3 O H sing 0.97 N N
20 O4 HO4 O H sing 0.97 N N



ARA : Used in PDB Entries

Total Number of PDB Entries: 17
Ligand Code PDB Entry ID Type Total Distinct
ARA 1abe Open in New Window Bound ligand 1 1
ARA 1bap Open in New Window Bound ligand 1 1
ARA 1ppm Open in New Window Bound ligand 1 1
ARA 2arc Open in New Window Bound ligand 2 1
ARA 2e1s Open in New Window Bound ligand 1 1
ARA 3a22 Open in New Window Bound ligand 9 1
ARA 3das Open in New Window Bound ligand 2 1
ARA 4rxt Open in New Window Bound ligand 1 1
ARA 5deq Open in New Window Bound ligand 2 1
ARA 5glo Open in New Window Bound ligand 2 1
ARA 5glp Open in New Window Bound ligand 4 1
ARA 5glr Open in New Window Bound ligand 1 1
ARA 5la0 Open in New Window Bound ligand 2 1
ARA 5mui Open in New Window Bound ligand 1 1
ARA 5muj Open in New Window Bound ligand 1 1
ARA 5mwk Open in New Window Bound ligand 1 1
ARA 6abp Open in New Window Bound ligand 1 1