Ligand profile

VB1

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: VK055_4546 — 2OG-Fe(II) oxygenase superfamily protein

Via homolog PDB 2vbp UniProt P05326 Formula C₁₃H₂₃N₃O₆S
Mol. weight 349.41 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
VB1
PDB
2vbp
UniProt (similar protein)
P05326
Target protein
VK055_4546

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 349.41 Da
LogP (Crippen) -1.04
H-bond donors 6
H-bond acceptors 6
TPSA 158.82 Ų
Rotatable bonds 11
Aromatic rings 0 / 0
Heavy atoms 23
Fraction sp³ C 0.69
Formula C₁₃H₂₃N₃O₆S

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 158.8
  • −1 ≤ LogP ≤ 5 -1.04
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 349.4
  • LogP ≤ 5 -1.04
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 158.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC[C@@H](C(=O)O)NC(=O)[C@H](CS)NC(=O)CCC[C@@H](C(=O)O)N
InChI 
InChI=1S/C13H23N3O6S/c1-2-8(13(21)22)16-11(18)9(6-23)15-10(17)5-3-4-7(14)12(19)20/h7-9,23H,2-6,14H2,1H3,(H,15,17)(H,16,18)(H,19,20)(H,21,22)/t7-,8-,9-/m0/s1
InChIKey 
UATNWSMKVYUEOE-CIUDSAMLSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF03171' 'PF14226

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_4546.

PDB 31

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)