Ligand profile

ZINC9391931

Virtual-screening candidate from ZINC.

Bound to: VK055_4127 — phosphoglycerate kinase family protein

Via homolog UniProt P07378 Formula C₂₅H₂₆N₄O₃S
Tanimoto 0.86
Mol. weight 462.58 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC9391931
UniProt (similar protein)
P07378
Tanimoto
0.864
Target protein
VK055_4127

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 462.58 Da
LogP (Crippen) 4.72
H-bond donors 2
H-bond acceptors 6
TPSA 89.16 Ų
Rotatable bonds 8
Aromatic rings 4 / 4
Heavy atoms 33
Fraction sp³ C 0.24
Formula C₂₅H₂₆N₄O₃S

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 89.2
  • −1 ≤ LogP ≤ 5 4.72
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 462.6
  • LogP ≤ 5 4.72
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 89.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc(C)cc(C(=O)NCCn2cc(SCC(=O)Nc3cc(C)on3)c3ccccc32)c1
InChI 
InChI=1S/C25H26N4O3S/c1-16-10-17(2)12-19(11-16)25(31)26-8-9-29-14-22(20-6-4-5-7-21(20)29)33-15-24(30)27-23-13-18(3)32-28-23/h4-7,10-14H,8-9,15H2,1-3H3,(H,26,31)(H,27,28,30)
InChIKey 
KLVOQVXCPTYHOS-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
CHEMBL1586947
Homolog
P07378

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_4127.

PDB 4

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 49

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

Compound Similarity (Tanimoto)