Ligand profile

L3A

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

Bound to: VK055_0680 — dipeptidase AC. Metallo peptidase

Via homolog PDB 3s2j UniProt Q93J45 Formula C₉H₂₀NO₄P
Mol. weight 237.24 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
L3A
PDB
3s2j
UniProt (similar protein)
Q93J45
Target protein
VK055_0680

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 237.24 Da
LogP (Crippen) 1.31
H-bond donors 3
H-bond acceptors 3
TPSA 100.62 Ų
Rotatable bonds 6
Aromatic rings 0 / 0
Heavy atoms 15
Fraction sp³ C 0.89
Formula C₉H₂₀NO₄P

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 100.6
  • −1 ≤ LogP ≤ 5 1.31
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 237.2
  • LogP ≤ 5 1.31
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 100.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H](CP(=O)([C@H](CC(C)C)N)O)C(=O)O
InChI 
InChI=1S/C9H20NO4P/c1-6(2)4-8(10)15(13,14)5-7(3)9(11)12/h6-8H,4-5,10H2,1-3H3,(H,11,12)(H,13,14)/t7-,8+/m0/s1
InChIKey 
PYHFMEIRRPJIRC-JGVFFNPUSA-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
PF01244

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_0680.

PDB 6

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)