Chemical Components in the PDB

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LPA : Summary

Code

LPA

One-letter code

X

Molecule name

LIPOIC ACID

Synonyms

5-[(3R)-1,2-dithiolan-3-yl]pentanoic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 5-[(3R)-1,2-dithiolan-3-yl]pentanoic acid
OpenEye OEToolkits 1.7.2 5-[(3R)-1,2-dithiolan-3-yl]pentanoic acid

Formula

C8 H14 O2 S2

Formal charge

0

Molecular weight

206.326 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)CCCCC1SSCC1
SMILES CACTVS 3.370 OC(=O)CCCC[CH]1CCSS1
SMILES OpenEye OEToolkits 1.7.2 C1CSSC1CCCCC(=O)O
Canonical SMILES CACTVS 3.370 OC(=O)CCCC[C@@H]1CCSS1
Canonical SMILES OpenEye OEToolkits 1.7.2 C1CSS[C@@H]1CCCCC(=O)O

IUPAC InChI

InChI=1S/C8H14O2S2/c9-8(10)4-2-1-3-7-5-6-11-12-7/h7H,1-6H2,(H,9,10)/t7-/m1/s1

IUPAC InChI key

AGBQKNBQESQNJD-SSDOTTSWSA-N
LPA

wwPDB Information

Atom count

26 (12 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



LPA : Atoms of Molecule

Total Number of Atoms: 26
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 4.586 0.088 -0.141
2 O1 O O1 N N N 0 5.707 0.729 0.222
3 C2 C C2 N N N 0 3.273 0.437 0.51
4 O2 O O2 N N N 0 4.628 -0.767 -0.995
5 C3 C C3 N N N 0 2.161 -0.429 -0.085
6 C4 C C4 N N N 0 0.828 -0.074 0.577
7 C5 C C5 N N N 0 -0.284 -0.94 -0.018
8 C6 C C6 R N N 0 -1.617 -0.585 0.644
9 S6 S S6 N N N 0 -2.092 1.123 0.189
10 C7 C C7 N N N 0 -2.701 -1.55 0.162
11 C8 C C8 N N N 0 -4.121 -0.951 0.211
12 S8 S S8 N N N 0 -3.941 0.676 -0.635
13 HO1 H HO1 N N N 0 6.524 0.473 -0.227
14 H2 H H2 N N N 0 3.34 0.256 1.583
15 H2A H H2A N N N 0 3.048 1.489 0.333
16 H3 H H3 N N N 0 2.094 -0.247 -1.158
17 H3A H H3A N N N 0 2.386 -1.481 0.092
18 H4 H H4 N N N 0 0.895 -0.256 1.65
19 H4A H H4A N N N 0 0.603 0.978 0.4
20 H5 H H5 N N N 0 -0.351 -0.759 -1.091
21 H5A H H5A N N N 0 -0.059 -1.992 0.159
22 H6 H H6 N N N 0 -1.519 -0.661 1.727
23 H7 H H7 N N N 0 -2.48 -1.841 -0.865
24 H7A H H7A N N N 0 -2.68 -2.442 0.789
25 H8 H H8 N N N 0 -4.824 -1.587 -0.328
26 H8A H H8A N N N 0 -4.443 -0.812 1.243



LPA : Chemical Bonds

Total Number of Bonds: 26
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C2 C1 C C sing 1.51 N N
2 C1 O2 C O doub 1.21 N N
3 C1 O1 C O sing 1.34 N N
4 O1 HO1 O H sing 0.97 N N
5 C3 C2 C C sing 1.53 N N
6 C2 H2 C H sing 1.09 N N
7 C2 H2A C H sing 1.09 N N
8 C4 C3 C C sing 1.53 N N
9 C3 H3 C H sing 1.09 N N
10 C3 H3A C H sing 1.09 N N
11 C5 C4 C C sing 1.53 N N
12 C4 H4 C H sing 1.09 N N
13 C4 H4A C H sing 1.09 N N
14 C6 C5 C C sing 1.53 N N
15 C5 H5 C H sing 1.09 N N
16 C5 H5A C H sing 1.09 N N
17 C7 C6 C C sing 1.53 N N
18 C6 S6 C S sing 1.83 N N
19 C6 H6 C H sing 1.09 N N
20 S8 S6 S S sing 2.07 N N
21 C8 C7 C C sing 1.54 N N
22 C7 H7 C H sing 1.09 N N
23 C7 H7A C H sing 1.09 N N
24 C8 S8 C S sing 1.84 N N
25 C8 H8 C H sing 1.09 N N
26 C8 H8A C H sing 1.09 N N



LPA : Used in PDB Entries

Total Number of PDB Entries: 10
Ligand Code PDB Entry ID Type Total Distinct
LPA 1hpc Open in New Window Bound ligand 1 1
LPA 1x2h Open in New Window Bound ligand 2 1
LPA 2art Open in New Window Bound ligand 1 1
LPA 2c8m Open in New Window Bound ligand 4 1
LPA 2iqd Open in New Window Bound ligand 1 1
LPA 5iby Open in New Window Bound ligand 1 1
LPA 5ij6 Open in New Window Bound ligand 1 1
LPA 5t8u Open in New Window Bound ligand 2 1
LPA 7yva Open in New Window Bound ligand 1 1
LPA 8cri Open in New Window Bound ligand 1 1