Ligand profile

40K

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

Bound to: VK055_5034 — UDP-galactopyranose mutase

Via homolog PDB 4xgk UniProt Q6NER4 Formula C₁₆H₁₁ClN₄O₂S₂
Mol. weight 390.88 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
40K
PDB
4xgk
UniProt (similar protein)
Q6NER4
Target protein
VK055_5034

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 390.88 Da
LogP (Crippen) 3.86
H-bond donors 1
H-bond acceptors 7
TPSA 80.37 Ų
Rotatable bonds 4
Aromatic rings 3 / 4
Heavy atoms 25
Fraction sp³ C 0.12
Formula C₁₆H₁₁ClN₄O₂S₂

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 80.4
  • −1 ≤ LogP ≤ 5 3.86
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 390.9
  • LogP ≤ 5 3.86
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 80.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(sc1)c2nnc3n2N=C([C@@H](S3)CC(=O)O)c4ccc(cc4)Cl
InChI 
InChI=1S/C16H11ClN4O2S2/c17-10-5-3-9(4-6-10)14-12(8-13(22)23)25-16-19-18-15(21(16)20-14)11-2-1-7-24-11/h1-7,12H,8H2,(H,22,23)/t12-/m0/s1
InChIKey 
PIDZXRXAOSMZRQ-LBPRGKRZSA-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
PF03275

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_5034.

PDB 7

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)