Ligand profile

2B6

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

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

Via homolog PDB 4mqq UniProt P9WQ81 Formula C₁₆H₁₅N₄O₆PS
Mol. weight 422.36 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
2B6
PDB
4mqq
UniProt (similar protein)
P9WQ81
Target protein
VK055_1732

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 422.36 Da
LogP (Crippen) 3.11
H-bond donors 3
H-bond acceptors 8
TPSA 154.56 Ų
Rotatable bonds 6
Aromatic rings 3 / 3
Heavy atoms 28
Fraction sp³ C 0.19
Formula C₁₆H₁₅N₄O₆PS

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 154.6
  • −1 ≤ LogP ≤ 5 3.11
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 422.4
  • LogP ≤ 5 3.11
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 154.6
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/C(=O)c2nc3ccccc3s2)O
InChI 
InChI=1S/C16H15N4O6PS/c1-9-14(21)11(10(6-17-9)8-26-27(23,24)25)7-18-20-15(22)16-19-12-4-2-3-5-13(12)28-16/h2-6,21H,7-8H2,1H3,(H2,23,24,25)/b20-18+
InChIKey 
GUGJKPFDBSWCQD-CZIZESTLSA-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)