Chemical Components in the PDB

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VLL : Summary

Code

VLL

One-letter code

X

Molecule name

(2S)-2,3-DIAMINOBUTANOIC ACID

Synonyms

L-THREO-2,3-DIAMINO-BUTYRIC ACID

Systematic names

ProgramVersionName
ACDLabs 11.02 (2S,3R)-2,3-diaminobutanoic acid
OpenEye OEToolkits 1.6.1 (2S,3R)-2,3-bis(azanyl)butanoic acid

Formula

C4 H10 N2 O2

Formal charge

0

Molecular weight

118.134 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 11.02 O=C(O)C(N)C(N)C
SMILES CACTVS 3.352 C[CH](N)[CH](N)C(O)=O
SMILES OpenEye OEToolkits 1.7.0 CC(C(C(=O)O)N)N
Canonical SMILES CACTVS 3.352 C[C@@H](N)[C@H](N)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.0 C[C@H]([C@@H](C(=O)O)N)N

IUPAC InChI

InChI=1S/C4H10N2O2/c1-2(5)3(6)4(7)8/h2-3H,5-6H2,1H3,(H,7,8)/t2-,3+/m1/s1

IUPAC InChI key

SXGMVGOVILIERA-GBXIJSLDSA-N
VLL

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

UNK

Defined at

2004-07-16

Last modified at

2023-11-03

Status

Released

Obsoleted

Not Assigned



VLL : 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 N N N N N N 0 -0.197 1.884 0.324
2 CA C CA S N N 0 -0.094 0.427 0.479
3 CB C CB R N N 0 -1.171 -0.254 -0.368
4 CG1 C CG1 N N N 0 -1.145 -1.762 -0.11
5 C C C N N N 0 1.267 -0.032 0.023
6 OXT O OXT N N Y 0 1.746 -1.219 0.429
7 O O O N N N 0 1.928 0.668 -0.707
8 NG2 N NG2 N N N 0 -2.49 0.282 -0.005
9 H H HN1 N N N 0 0.462 2.359 0.922
10 H2 H HN2 N N Y 0 -0.07 2.155 -0.64
11 HA H HA N N N 0 -0.235 0.163 1.527
12 HB H HB N N N 0 -0.979 -0.062 -1.423
13 HG11 H HG11 N N N 0 -1.913 -2.246 -0.713
14 HG12 H HG12 N N N 0 -0.167 -2.159 -0.379
15 HG13 H HG13 N N N 0 -1.338 -1.953 0.946
16 HXT H HXT N N Y 0 2.624 -1.47 0.11
17 HG21 H HG21 N N N 0 -2.512 1.286 -0.105
18 HG22 H HG22 N N Y 0 -3.219 -0.152 -0.551



VLL : 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 N CA N C sing 1.47 N N
2 N H N H sing 1.01 N N
3 N H2 N H sing 1.01 N N
4 CA CB C C sing 1.53 N N
5 CA C C C sing 1.51 N N
6 CA HA C H sing 1.09 N N
7 CB CG1 C C sing 1.53 N N
8 CB NG2 C N sing 1.47 N N
9 CB HB C H sing 1.09 N N
10 CG1 HG11 C H sing 1.09 N N
11 CG1 HG12 C H sing 1.09 N N
12 CG1 HG13 C H sing 1.09 N N
13 C OXT C O sing 1.34 N N
14 C O C O doub 1.21 N N
15 OXT HXT O H sing 0.97 N N
16 NG2 HG21 N H sing 1.01 N N
17 NG2 HG22 N H sing 1.01 N N



VLL : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
VLL 1w3m Open in New Window Polymer component 12 1