Chemical Components in the PDB

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VOL : Summary

Code

VOL

One-letter code

X

Molecule name

L-VALINOL

Systematic names

ProgramVersionName
ACDLabs 10.04 (2S)-2-amino-3-methylbutan-1-ol
OpenEye OEToolkits 1.5.0 (2S)-2-amino-3-methyl-butan-1-ol

Formula

C5 H13 N O

Formal charge

0

Molecular weight

103.163 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 OCC(N)C(C)C
SMILES CACTVS 3.341 CC(C)[CH](N)CO
SMILES OpenEye OEToolkits 1.5.0 CC(C)C(CO)N
Canonical SMILES CACTVS 3.341 CC(C)[C@H](N)CO
Canonical SMILES OpenEye OEToolkits 1.5.0 CC(C)[C@@H](CO)N

IUPAC InChI

InChI=1S/C5H13NO/c1-4(2)5(6)3-7/h4-5,7H,3,6H2,1-2H3/t5-/m1/s1

IUPAC InChI key

NWYYWIJOWOLJNR-RXMQYKEDSA-N
VOL

wwPDB Information

Atom count

20 (7 without Hydrogen)

Polymer type

Amino Acid

Type description

L-PEPTIDE LINKING

Type code

ATOMP

Is modified

Yes

Standard parent

UNK

Defined at

2002-06-26

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



VOL : 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 N N N N N N 0 -1.177 -0.9 -0.198
2 CA C CA S N N 0 -0.383 0.335 -0.213
3 CB C CB N N N 0 0.364 0.477 1.113
4 CG1 C CG1 N N N 0 -0.643 0.533 2.263
5 CG2 C CG2 N N N 0 1.293 -0.722 1.306
6 CH2 C CH2 N N N 0 0.623 0.28 -1.363
7 OH O OH N N N 0 -0.074 0.147 -2.603
8 HN1 H 1HN N N N 0 -0.527 -1.661 -0.069
9 HN2 H 2HN N N N 0 -1.751 -0.866 0.63
10 HA H HA N N N 0 -1.045 1.19 -0.351
11 HB H HB N N N 0 0.953 1.394 1.102
12 HG1 H HG1 N N N 0 -0.11 0.634 3.208
13 HG2 H HG2 N N N 0 -1.305 1.388 2.125
14 HG3 H HG3 N N N 0 -1.232 -0.384 2.274
15 H21 H H21 N N N 0 0.704 -1.639 1.317
16 H22 H H22 N N N 0 2.01 -0.762 0.487
17 H23 H H23 N N N 0 1.825 -0.621 2.252
18 HH1 H HH1 N N N 0 1.285 -0.575 -1.226
19 HH2 H HH2 N N N 0 1.212 1.197 -1.375
20 HH H HH N N N 0 0.595 0.116 -3.299



VOL : Chemical Bonds

Total Number of Bonds: 19
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N CA N C sing 1.47 N N
2 N HN1 N H sing 1.01 N N
3 N HN2 N H sing 1.01 N N
4 CA CB C C sing 1.53 N N
5 CA CH2 C C sing 1.53 N N
6 CA HA C H sing 1.09 N N
7 CB CG1 C C sing 1.53 N N
8 CB CG2 C C sing 1.53 N N
9 CB HB C H sing 1.09 N N
10 CG1 HG1 C H sing 1.09 N N
11 CG1 HG2 C H sing 1.09 N N
12 CG1 HG3 C H sing 1.09 N N
13 CG2 H21 C H sing 1.09 N N
14 CG2 H22 C H sing 1.09 N N
15 CG2 H23 C H sing 1.09 N N
16 CH2 OH C O sing 1.43 N N
17 CH2 HH1 C H sing 1.09 N N
18 CH2 HH2 C H sing 1.09 N N
19 OH HH O H sing 0.97 N N



VOL : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
VOL 1m24 Open in New Window Polymer component 2 1
VOL 4y70 Open in New Window Polymer component 4 1