Ligand profile

2B1

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

Bound to: VK055_1732 — adenosylmethionine-8-amino-7-oxononanoate transaminase

Via homolog PDB 4mqp UniProt P9WQ81 Formula C₁₅H₁₅N₄O₅PS
Mol. weight 394.35 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
2B1
PDB
4mqp
UniProt (similar protein)
P9WQ81
Target protein
VK055_1732

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 394.35 Da
LogP (Crippen) 3.60
H-bond donors 3
H-bond acceptors 8
TPSA 137.49 Ų
Rotatable bonds 6
Aromatic rings 3 / 3
Heavy atoms 26
Fraction sp³ C 0.20
Formula C₁₅H₁₅N₄O₅PS

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 137.5
  • −1 ≤ LogP ≤ 5 3.60
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 394.3
  • LogP ≤ 5 3.60
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 137.5
PAINS Alert

Matches PAINS filter: azo_A(324). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c(cn1)COP(=O)(O)O)C/N=N/c2nc3ccccc3s2)O
InChI 
InChI=1S/C15H15N4O5PS/c1-9-14(20)11(10(6-16-9)8-24-25(21,22)23)7-17-19-15-18-12-4-2-3-5-13(12)26-15/h2-6,20H,7-8H2,1H3,(H2,21,22,23)/b19-17+
InChIKey 
IRSQGYHNYSBCCK-HTXNQAPBSA-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
PF00202

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_1732.

PDB 25

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

Ligand PDB entry

ChEMBL 100

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

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)