Ligand profile

B88

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

Bound to: VK055_0680 — dipeptidase AC. Metallo peptidase

Via homolog PDB 3isi UniProt Q93J45 Formula C₇H₁₄NO₆P
Mol. weight 239.16 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
B88
PDB
3isi
UniProt (similar protein)
Q93J45
Target protein
VK055_0680

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 239.16 Da
LogP (Crippen) -0.26
H-bond donors 4
H-bond acceptors 4
TPSA 137.92 Ų
Rotatable bonds 6
Aromatic rings 0 / 0
Heavy atoms 15
Fraction sp³ C 0.71
Formula C₇H₁₄NO₆P

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 137.9
  • −1 ≤ LogP ≤ 5 -0.26
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 239.2
  • LogP ≤ 5 -0.26
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 137.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H](N)[P@](=O)(C[C@@H](CC(=O)O)C(=O)O)O
InChI 
InChI=1S/C7H14NO6P/c1-4(8)15(13,14)3-5(7(11)12)2-6(9)10/h4-5H,2-3,8H2,1H3,(H,9,10)(H,11,12)(H,13,14)/t4-,5-/m1/s1
InChIKey 
LWODXTSWCZWQHR-RFZPGFLSSA-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)