Ligand profile

PXM

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

Bound to: VK055_4745 — pyridoxal kinase

Via homolog PDB 6k90 UniProt A0A3S7X3C0 Formula C₈H₁₂N₂O₂
Mol. weight 168.20 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PXM
PDB
6k90
UniProt (similar protein)
A0A3S7X3C0
Target protein
VK055_4745

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 168.20 Da
LogP (Crippen) 0.05
H-bond donors 3
H-bond acceptors 4
TPSA 79.37 Ų
Rotatable bonds 2
Aromatic rings 1 / 1
Heavy atoms 12
Fraction sp³ C 0.38
Formula C₈H₁₂N₂O₂

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 79.4
  • −1 ≤ LogP ≤ 5 0.05
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 168.2
  • LogP ≤ 5 0.05
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 79.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c(cn1)CO)CN)O
InChI 
InChI=1S/C8H12N2O2/c1-5-8(12)7(2-9)6(4-11)3-10-5/h3,11-12H,2,4,9H2,1H3
InChIKey 
NHZMQXZHNVQTQA-UHFFFAOYSA-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
PF08543

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_4745.

PDB 7

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

Ligand PDB entry

ChEMBL 5

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)