Ligand profile

XP0

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

Bound to: VK055_0984 — hypothetical protein

Via homolog PDB 4clo UniProt O76290 Formula C₁₈H₁₇N₅
Mol. weight 303.37 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
XP0
PDB
4clo
UniProt (similar protein)
O76290
Target protein
VK055_0984

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 303.37 Da
LogP (Crippen) 2.54
H-bond donors 2
H-bond acceptors 4
TPSA 70.83 Ų
Rotatable bonds 1
Aromatic rings 3 / 4
Heavy atoms 23
Fraction sp³ C 0.22
Formula C₁₈H₁₇N₅

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 70.8
  • −1 ≤ LogP ≤ 5 2.54
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 303.4
  • LogP ≤ 5 2.54
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 70.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)C#Cc2c[nH]c3c2c(nc(n3)N)N4CCCC4
InChI 
InChI=1S/C18H17N5/c19-18-21-16-15(17(22-18)23-10-4-5-11-23)14(12-20-16)9-8-13-6-2-1-3-7-13/h1-3,6-7,12H,4-5,10-11H2,(H3,19,20,21,22)
InChIKey 
PFDYIZWUJSPGHR-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
PF13561

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_0984.

PDB 92

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

Ligand PDB entry

ChEMBL 35

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)