Chemical Components in the PDB

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VAD : Summary

Code

VAD

One-letter code

V

Molecule name

DEAMINOHYDROXYVALINE

Systematic names

ProgramVersionName
ACDLabs 10.04 (2R)-2-hydroxy-3-methylbutanoic acid
OpenEye OEToolkits 1.5.0 (2R)-2-hydroxy-3-methyl-butanoic acid

Formula

C5 H10 O3

Formal charge

0

Molecular weight

118.131 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)C(O)C(C)C
SMILES CACTVS 3.341 CC(C)[CH](O)C(O)=O
SMILES OpenEye OEToolkits 1.5.0 CC(C)C(C(=O)O)O
Canonical SMILES CACTVS 3.341 CC(C)[C@@H](O)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 CC(C)[C@H](C(=O)O)O

IUPAC InChI

InChI=1S/C5H10O3/c1-3(2)4(6)5(7)8/h3-4,6H,1-2H3,(H,7,8)/t4-/m1/s1

IUPAC InChI key

NGEWQZIDQIYUNV-SCSAIBSYSA-N
VAD

wwPDB Information

Atom count

18 (8 without Hydrogen)

Polymer type

Amino Acid

Type description

L-PEPTIDE LINKING

Type code

ATOMP

Is modified

Yes

Standard parent

VAL

Defined at

1999-07-08

Last modified at

2023-11-03

Status

Released

Obsoleted

Not Assigned



VAD : Atoms of Molecule

Total Number of Atoms: 18
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 CA C CA R N N 0 -0.482 -0.436 0.101
2 CB C CB N N N 0 0.23 0.38 1.18
3 CG1 C CG1 N N N 0 -0.323 0.002 2.555
4 CG2 C CG2 N N N 0 1.731 0.083 1.135
5 C C C N N N 0 0.062 -0.064 -1.253
6 O O O N N N 0 -0.672 0.391 -2.096
7 OXT O OXT N N Y 0 1.366 -0.238 -1.523
8 OE O OE N N N 0 -1.884 -0.159 0.142
9 HA H HA N N N 0 -0.316 -1.498 0.28
10 HB H HB N N N 0 0.065 1.442 1.001
11 HG11 H 1HG1 N N N 0 0.185 0.584 3.324
12 HG12 H 2HG1 N N N 0 -1.391 0.213 2.587
13 HG13 H 3HG1 N N N 0 -0.157 -1.06 2.734
14 HXT H HXT N N Y 0 1.716 0.0 -2.392
15 HG21 H 1HG2 N N N 0 1.897 -0.978 1.314
16 HG22 H 2HG2 N N N 0 2.125 0.353 0.155
17 HG23 H 3HG2 N N N 0 2.239 0.665 1.904
18 HOE H HOE N N Y 0 -1.986 0.788 -0.02



VAD : Chemical Bonds

Total Number of Bonds: 17
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CA CB C C sing 1.53 N N
2 CA C C C sing 1.51 N N
3 CA OE C O sing 1.43 N N
4 CA HA C H sing 1.09 N N
5 CB CG1 C C sing 1.53 N N
6 CB CG2 C C sing 1.53 N N
7 CB HB C H sing 1.09 N N
8 CG1 HG11 C H sing 1.09 N N
9 CG1 HG12 C H sing 1.09 N N
10 CG1 HG13 C H sing 1.09 N N
11 CG2 HG21 C H sing 1.09 N N
12 CG2 HG22 C H sing 1.09 N N
13 CG2 HG23 C H sing 1.09 N N
14 C O C O doub 1.21 N N
15 C OXT C O sing 1.34 N N
16 OXT HXT O H sing 0.97 N N
17 OE HOE O H sing 0.97 N N



VAD : Used in PDB Entries

Total Number of PDB Entries: 5
Ligand Code PDB Entry ID Type Total Distinct
VAD 1cwo Open in New Window Polymer component 1 1
VAD 6ecd Open in New Window Polymer component 1 1
VAD 6ece Open in New Window Polymer component 6 3
VAD 6ecf Open in New Window Polymer component 18 3
VAD 8jdp Open in New Window Bound ligand 1 1