Ligand profile

ZINC5663672

Virtual-screening candidate from ZINC.

Bound to: VK055_4988 — bacterial extracellular solute-binding, 5 Middlefamily protein

Via homolog UniProt B8F653 Formula C₁₈H₂₄N₄O₈S
Tanimoto 0.61
Mol. weight 456.48 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC5663672
UniProt (similar protein)
B8F653
Tanimoto
0.611
Target protein
VK055_4988

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 456.48 Da
LogP (Crippen) -1.06
H-bond donors 7
H-bond acceptors 8
TPSA 208.15 Ų
Rotatable bonds 13
Aromatic rings 1 / 1
Heavy atoms 31
Fraction sp³ C 0.39
Formula C₁₈H₂₄N₄O₈S

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

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 208.1
  • −1 ≤ LogP ≤ 5 -1.06
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 456.5
  • LogP ≤ 5 -1.06
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 13
  • TPSA ≤ 140 Ų 208.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
N[C@@H](CCC(=O)N[C@H](CSCC(=O)Nc1ccc(O)cc1)C(=O)NCC(=O)O)C(=O)O
InChI 
InChI=1S/C18H24N4O8S/c19-12(18(29)30)5-6-14(24)22-13(17(28)20-7-16(26)27)8-31-9-15(25)21-10-1-3-11(23)4-2-10/h1-4,12-13,23H,5-9,19H2,(H,20,28)(H,21,25)(H,22,24)(H,26,27)(H,29,30)/t12-,13+/m0/s1
InChIKey 
SERPYWCCDHWSRV-QWHCGFSZSA-N

Provenance

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

Method
LigQ nearest_k
Query
GDS
Homolog
B8F653

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_4988.

PDB 4

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)