Ligand profile

ZINC6559724

Virtual-screening candidate from ZINC.

Bound to: VK055_4900 — nudix-type nucleoside diphosphatase, YffH/AdpP family protein

Via homolog UniProt Q9UKK9 Formula C₁₁H₁₅N₅
Tanimoto 0.90
Mol. weight 217.28 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC6559724
UniProt (similar protein)
Q9UKK9
Tanimoto
0.897
Target protein
VK055_4900

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 217.28 Da
LogP (Crippen) 1.73
H-bond donors 1
H-bond acceptors 4
TPSA 57.70 Ų
Rotatable bonds 1
Aromatic rings 2 / 3
Heavy atoms 16
Fraction sp³ C 0.55
Formula C₁₁H₁₅N₅

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 57.7
  • −1 ≤ LogP ≤ 5 1.73
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 217.3
  • LogP ≤ 5 1.73
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 57.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(N2CCCCCC2)c2nc[nH]c2n1
InChI 
InChI=1S/C11H15N5/c1-2-4-6-16(5-3-1)11-9-10(13-7-12-9)14-8-15-11/h7-8H,1-6H2,(H,12,13,14,15)
InChIKey 
LPDNHQZTRVRLOW-UHFFFAOYSA-N

Provenance

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

Method
LigQ nearest_k
Query
K1D
Homolog
Q9UKK9

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_4900.

PDB 54

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 49

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

Compound Similarity (Tanimoto)