Ligand profile

W16

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

Bound to: VK055_0984 — hypothetical protein

Via homolog PDB 2yhi UniProt Q581W1 Formula C₄H₆ClN₃S
Mol. weight 163.63 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
W16
PDB
2yhi
UniProt (similar protein)
Q581W1
Target protein
VK055_0984

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 163.63 Da
LogP (Crippen) 0.90
H-bond donors 1
H-bond acceptors 4
TPSA 51.80 Ų
Rotatable bonds 2
Aromatic rings 1 / 1
Heavy atoms 9
Fraction sp³ C 0.50
Formula C₄H₆ClN₃S

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 51.8
  • −1 ≤ LogP ≤ 5 0.90
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 163.6
  • LogP ≤ 5 0.90
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 51.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CCl)c1nnc(s1)N
InChI 
InChI=1S/C4H6ClN3S/c5-2-1-3-7-8-4(6)9-3/h1-2H2,(H2,6,8)
InChIKey 
XGIWQRDVHNRICP-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)