Ligand profile

01B

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

Bound to: VK055_4139 — pepP

Via homolog PDB 5x49 UniProt Q9NQH7 Formula C₁₀H₁₃NO₃
Mol. weight 195.22 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
01B
PDB
5x49
UniProt (similar protein)
Q9NQH7
Target protein
VK055_4139

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 195.22 Da
LogP (Crippen) 0.00
H-bond donors 3
H-bond acceptors 3
TPSA 83.55 Ų
Rotatable bonds 4
Aromatic rings 1 / 1
Heavy atoms 14
Fraction sp³ C 0.30
Formula C₁₀H₁₃NO₃

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 83.5
  • −1 ≤ LogP ≤ 5 0.00
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 195.2
  • LogP ≤ 5 0.00
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 83.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)C[C@H]([C@@H](C(=O)O)O)N
InChI 
InChI=1S/C10H13NO3/c11-8(9(12)10(13)14)6-7-4-2-1-3-5-7/h1-5,8-9,12H,6,11H2,(H,13,14)/t8-,9+/m1/s1
InChIKey 
LDSJMFGYNFIFRK-BDAKNGLRSA-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
PF00557' 'PF05195

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_4139.

PDB 4

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)