Chemical Components in the PDB

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LPM : Summary

Code

LPM

One-letter code

X

Molecule name

6,8-DIMERCAPTO-OCTANOIC ACID AMIDE

Systematic names

ProgramVersionName
ACDLabs 10.04 (6R)-6,8-disulfanyloctanamide
OpenEye OEToolkits 1.5.0 (6R)-6,8-bis-sulfanyloctanamide

Formula

C8 H17 N O S2

Formal charge

0

Molecular weight

207.357 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(N)CCCCC(S)CCS
SMILES CACTVS 3.341 NC(=O)CCCC[CH](S)CCS
SMILES OpenEye OEToolkits 1.5.0 C(CCC(=O)N)CC(CCS)S
Canonical SMILES CACTVS 3.341 NC(=O)CCCC[C@@H](S)CCS
Canonical SMILES OpenEye OEToolkits 1.5.0 C(CCC(=O)N)C[C@H](CCS)S

IUPAC InChI

InChI=1S/C8H17NOS2/c9-8(10)4-2-1-3-7(12)5-6-11/h7,11-12H,1-6H2,(H2,9,10)/t7-/m1/s1

IUPAC InChI key

VLYUGYAKYZETRF-SSDOTTSWSA-N
LPM

wwPDB Information

Atom count

29 (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

2011-06-04

Status

Released

Obsoleted

Not Assigned



LPM : Atoms of Molecule

Total Number of Atoms: 29
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 0.304 0.035 4.88
2 O O O N N N 0 1.366 0.618 4.813
3 N N N N N N 0 -0.242 -0.232 6.082
4 C2 C C2 N N N 0 -0.402 -0.389 3.619
5 C3 C C3 N N N 0 0.425 0.031 2.403
6 C4 C C4 N N N 0 -0.293 -0.399 1.123
7 C5 C C5 N N N 0 0.534 0.021 -0.092
8 C6 C C6 R N N 0 -0.183 -0.41 -1.372
9 S6 S S6 N N N 0 -1.814 0.38 -1.447
10 C7 C C7 N N N 0 0.644 0.011 -2.588
11 C8 C C8 N N N 0 -0.074 -0.42 -3.868
12 S8 S S8 N N N 0 0.907 0.079 -5.31
13 HN1 H 1HN N N N 0 0.212 0.041 6.894
14 HN2 H 2HN N N N 0 -1.093 -0.694 6.136
15 H21 H 1H2 N N N 0 -0.523 -1.473 3.618
16 H22 H 2H2 N N N 0 -1.382 0.085 3.574
17 H31 H 1H3 N N N 0 0.546 1.115 2.404
18 H32 H 2H3 N N N 0 1.404 -0.443 2.448
19 H41 H 1H4 N N N 0 -0.414 -1.483 1.122
20 H42 H 2H4 N N N 0 -1.272 0.075 1.078
21 H51 H 1H5 N N N 0 0.655 1.105 -0.091
22 H52 H 2H5 N N N 0 1.514 -0.453 -0.047
23 H6 H H6 N N N 0 -0.304 -1.493 -1.373
24 HS6 H HS6 N N N 0 -1.447 1.674 -1.436
25 H71 H 1H7 N N N 0 0.765 1.094 -2.587
26 H72 H 2H7 N N N 0 1.623 -0.463 -2.543
27 H81 H 1H8 N N N 0 -0.195 -1.503 -3.869
28 H82 H 2H8 N N N 0 -1.053 0.055 -3.913
29 HS8 H HS8 N N N 0 0.12 -0.381 -6.299



LPM : Chemical Bonds

Total Number of Bonds: 28
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 O C O doub 1.21 N N
2 C1 N C N sing 1.35 N N
3 C1 C2 C C sing 1.51 N N
4 N HN1 N H sing 0.97 N N
5 N HN2 N H sing 0.97 N N
6 C2 C3 C C sing 1.53 N N
7 C2 H21 C H sing 1.09 N N
8 C2 H22 C H sing 1.09 N N
9 C3 C4 C C sing 1.53 N N
10 C3 H31 C H sing 1.09 N N
11 C3 H32 C H sing 1.09 N N
12 C4 C5 C C sing 1.53 N N
13 C4 H41 C H sing 1.09 N N
14 C4 H42 C H sing 1.09 N N
15 C5 C6 C C sing 1.53 N N
16 C5 H51 C H sing 1.09 N N
17 C5 H52 C H sing 1.09 N N
18 C6 S6 C S sing 1.81 N N
19 C6 C7 C C sing 1.53 N N
20 C6 H6 C H sing 1.09 N N
21 S6 HS6 S H sing 1.35 N N
22 C7 C8 C C sing 1.53 N N
23 C7 H71 C H sing 1.09 N N
24 C7 H72 C H sing 1.09 N N
25 C8 S8 C S sing 1.81 N N
26 C8 H81 C H sing 1.09 N N
27 C8 H82 C H sing 1.09 N N
28 S8 HS8 S H sing 1.35 N N



LPM : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
LPM 1eab Open in New Window Bound ligand 1 1
LPM 1eae Open in New Window Bound ligand 1 1
LPM 6zzk Open in New Window Bound ligand 1 1