Ligand profile

P5D

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

Bound to: VK055_0680 — dipeptidase AC. Metallo peptidase

Via homolog PDB 3s2m UniProt Q93J45 Formula C₁₃H₁₈NO₆P
Mol. weight 315.26 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
P5D
PDB
3s2m
UniProt (similar protein)
Q93J45
Target protein
VK055_0680

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 315.26 Da
LogP (Crippen) 0.96
H-bond donors 4
H-bond acceptors 4
TPSA 137.92 Ų
Rotatable bonds 8
Aromatic rings 1 / 1
Heavy atoms 21
Fraction sp³ C 0.38
Formula C₁₃H₁₈NO₆P

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 0.96
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 315.3
  • LogP ≤ 5 0.96
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 137.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)C[C@H](N)P(=O)(C[C@H](CC(=O)O)C(=O)O)O
InChI 
InChI=1S/C13H18NO6P/c14-11(6-9-4-2-1-3-5-9)21(19,20)8-10(13(17)18)7-12(15)16/h1-5,10-11H,6-8,14H2,(H,15,16)(H,17,18)(H,19,20)/t10-,11+/m0/s1
InChIKey 
HUMGCALEJILOSC-WDEREUQCSA-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)