Ligand profile

B33

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

Bound to: VK055_0172 — putative N-acetyltransferase

Via homolog PDB 2b4b UniProt P21673 Formula C₁₁H₂₇N₃
Mol. weight 201.36 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
B33
PDB
2b4b
UniProt (similar protein)
P21673
Target protein
VK055_0172

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 201.36 Da
LogP (Crippen) 0.97
H-bond donors 3
H-bond acceptors 3
TPSA 36.09 Ų
Rotatable bonds 11
Aromatic rings 0 / 0
Heavy atoms 14
Fraction sp³ C 1.00
Formula C₁₁H₂₇N₃

Drug-likeness

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

Permeability proxy High

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 36.1
  • −1 ≤ LogP ≤ 5 0.97
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 201.4
  • LogP ≤ 5 0.97
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 36.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCNCCCNCCCNCC
InChI 
InChI=1S/C11H27N3/c1-3-7-13-9-6-11-14-10-5-8-12-4-2/h12-14H,3-11H2,1-2H3
InChIKey 
ZFYULDAPZWEGGQ-UHFFFAOYSA-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
PF00583

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_0172.

PDB 1

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

Ligand PDB entry

ChEMBL 4

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 34

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

Compound Similarity (Tanimoto)