Chemical Components in the PDB

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SST : Summary

Code

SST

One-letter code

X

Molecule name

L-arabinitol

Systematic names

ProgramVersionName
ACDLabs 12.01 L-arabinitol
OpenEye OEToolkits 1.7.6 (2S,4S)-pentane-1,2,3,4,5-pentol

Formula

C5 H12 O5

Formal charge

0

Molecular weight

152.146 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 OC(CO)C(O)C(O)CO
SMILES CACTVS 3.385 OC[CH](O)[CH](O)[CH](O)CO
SMILES OpenEye OEToolkits 1.7.6 C(C(C(C(CO)O)O)O)O
Canonical SMILES CACTVS 3.385 OC[C@H](O)[C@@H](O)[C@@H](O)CO
Canonical SMILES OpenEye OEToolkits 1.7.6 C([C@@H](C([C@H](CO)O)O)O)O

IUPAC InChI

InChI=1S/C5H12O5/c6-1-3(8)5(10)4(9)2-7/h3-10H,1-2H2/t3-,4-/m0/s1

IUPAC InChI key

HEBKCHPVOIAQTA-IMJSIDKUSA-N
SST

wwPDB Information

Atom count

22 (10 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

ATOMS

Is modified

No

Standard parent

Not Assigned

Defined at

2014-09-02

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



SST : 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 O3 O O3 N N N 0 -0.079 -1.755 -0.106
2 O4 O O4 N N N 0 1.333 1.577 0.468
3 O2 O O2 N N N 0 -1.259 0.546 -1.361
4 O5 O O5 N N N 0 3.65 0.056 -0.293
5 O1 O O1 N N N 0 -3.653 0.388 0.222
6 C3 C C3 N N N 0 0.003 -0.441 0.449
7 C4 C C4 S N N 0 1.251 0.263 -0.088
8 C2 C C2 S N N 0 -1.242 0.358 0.056
9 C5 C C5 N N N 0 2.495 -0.536 0.306
10 C1 C C1 N N N 0 -2.495 -0.408 0.483
11 H1 H H1 N N N 0 -0.135 -1.771 -1.071
12 H2 H H2 N N N 0 1.389 1.593 1.433
13 H3 H H3 N N N 0 -1.276 -0.278 -1.867
14 H4 H H4 N N N 0 4.477 -0.399 -0.086
15 H5 H H5 N N N 0 -4.486 -0.036 0.469
16 H6 H H6 N N N 0 0.062 -0.508 1.536
17 H7 H H7 N N N 0 1.191 0.33 -1.174
18 H8 H H8 N N N 0 -1.222 1.328 0.551
19 H9 H H9 N N N 0 2.392 -1.564 -0.042
20 H10 H H10 N N N 0 2.604 -0.528 1.39
21 H11 H H11 N N N 0 -2.44 -0.629 1.549
22 H12 H H12 N N N 0 -2.561 -1.34 -0.078



SST : Chemical Bonds

Total Number of Bonds: 21
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O5 C5 O C sing 1.43 N N
2 C5 C4 C C sing 1.53 N N
3 O4 C4 O C sing 1.43 N N
4 C1 O1 C O sing 1.43 N N
5 C1 C2 C C sing 1.53 N N
6 C4 C3 C C sing 1.53 N N
7 C2 C3 C C sing 1.53 N N
8 C2 O2 C O sing 1.43 N N
9 C3 O3 C O sing 1.43 N N
10 O3 H1 O H sing 0.97 N N
11 O4 H2 O H sing 0.97 N N
12 O2 H3 O H sing 0.97 N N
13 O5 H4 O H sing 0.97 N N
14 O1 H5 O H sing 0.97 N N
15 C3 H6 C H sing 1.09 N N
16 C4 H7 C H sing 1.09 N N
17 C2 H8 C H sing 1.09 N N
18 C5 H9 C H sing 1.09 N N
19 C5 H10 C H sing 1.09 N N
20 C1 H11 C H sing 1.09 N N
21 C1 H12 C H sing 1.09 N N



SST : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
SST 4r1q Open in New Window Bound ligand 6 1