Ligand profile

09M

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

Bound to: VK055_0552 — fused predicted DNA-binding transcriptional regulator and predicted amino transferase

Via homolog PDB 3ue8 UniProt Q8N5Z0 Formula C₁₇H₁₈N₃O₇P
Mol. weight 407.32 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
09M
PDB
3ue8
UniProt (similar protein)
Q8N5Z0
Target protein
VK055_0552

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 407.32 Da
LogP (Crippen) 1.87
H-bond donors 5
H-bond acceptors 8
TPSA 154.14 Ų
Rotatable bonds 6
Aromatic rings 3 / 3
Heavy atoms 28
Fraction sp³ C 0.18
Formula C₁₇H₁₈N₃O₇P

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 154.1
  • −1 ≤ LogP ≤ 5 1.87
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 407.3
  • LogP ≤ 5 1.87
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 154.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c(cn1)COP(=O)(O)O)CNC2=Cc3ccccc3N(C2=O)O)O
InChI 
InChI=1S/C17H18N3O7P/c1-10-16(21)13(12(7-18-10)9-27-28(24,25)26)8-19-14-6-11-4-2-3-5-15(11)20(23)17(14)22/h2-7,19,21,23H,8-9H2,1H3,(H2,24,25,26)
InChIKey 
ZKPXUQQBRMXHLJ-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
PF00155

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_0552.

PDB 19

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)