Ligand profile

7B9

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

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

Via homolog PDB 5te2 UniProt P0A4X7 Formula C₁₆H₂₂N₃O₇P
Mol. weight 399.34 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
7B9
PDB
5te2
UniProt (similar protein)
P0A4X7
Target protein
VK055_1732

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 399.34 Da
LogP (Crippen) 0.93
H-bond donors 6
H-bond acceptors 7
TPSA 165.00 Ų
Rotatable bonds 9
Aromatic rings 2 / 2
Heavy atoms 27
Fraction sp³ C 0.38
Formula C₁₆H₂₂N₃O₇P

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 165.0
  • −1 ≤ LogP ≤ 5 0.93
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 399.3
  • LogP ≤ 5 0.93
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 165.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c(cn1)COP(=O)(O)O)CNC2=CNC(=CC2=O)CCCO)O
InChI 
InChI=1S/C16H22N3O7P/c1-10-16(22)13(11(6-17-10)9-26-27(23,24)25)7-19-14-8-18-12(3-2-4-20)5-15(14)21/h5-6,8,19-20,22H,2-4,7,9H2,1H3,(H,18,21)(H2,23,24,25)
InChIKey 
LWVUNNHCQMOSIS-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
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)