Ligand profile

ZINC639

Virtual-screening candidate from ZINC.

Bound to: VK055_4612 — pyridoxine 5'-phosphate synthase

Via homolog UniProt P0A794 Formula C₁₀H₁₃NO₆
Tanimoto 0.58
Mol. weight 243.21 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC639
UniProt (similar protein)
P0A794
Tanimoto
0.578
Target protein
VK055_4612

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 243.21 Da
LogP (Crippen) -0.49
H-bond donors 4
H-bond acceptors 6
TPSA 120.11 Ų
Rotatable bonds 5
Aromatic rings 1 / 1
Heavy atoms 17
Fraction sp³ C 0.40
Formula C₁₀H₁₃NO₆

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 120.1
  • −1 ≤ LogP ≤ 5 -0.49
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 243.2
  • LogP ≤ 5 -0.49
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 120.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ncc(CO[C@H](O)C(=O)O)c(CO)c1O
InChI 
InChI=1S/C10H13NO6/c1-5-8(13)7(3-12)6(2-11-5)4-17-10(16)9(14)15/h2,10,12-13,16H,3-4H2,1H3,(H,14,15)/t10-/m0/s1
InChIKey 
IZMRUZYKDJYBTG-JTQLQIEISA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Query
PXP
Homolog
P0A794

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_4612.

PDB 3

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)