Ligand profile

ZINC4962281

Virtual-screening candidate from ZINC.

Bound to: KP13_05440 — Peptide transport periplasmic protein sapA

Via homolog UniProt B8F653 Formula C₁₃H₂₃N₃O₆S
Tanimoto 0.73
Mol. weight 349.41 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC4962281
UniProt (similar protein)
B8F653
Tanimoto
0.733
Target protein
KP13_05440

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 349.41 Da
LogP (Crippen) -0.99
H-bond donors 5
H-bond acceptors 6
TPSA 158.82 Ų
Rotatable bonds 12
Aromatic rings 0 / 0
Heavy atoms 23
Fraction sp³ C 0.69
Formula C₁₃H₂₃N₃O₆S

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 158.8
  • −1 ≤ LogP ≤ 5 -0.99
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 349.4
  • LogP ≤ 5 -0.99
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 158.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCSC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=O)O
InChI 
InChI=1S/C13H23N3O6S/c1-2-5-23-7-9(12(20)15-6-11(18)19)16-10(17)4-3-8(14)13(21)22/h8-9H,2-7,14H2,1H3,(H,15,20)(H,16,17)(H,18,19)(H,21,22)/t8-,9-/m0/s1
InChIKey 
IJQSYVSEZCHJFD-IUCAKERBSA-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 KP13_05440.

PDB 5

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)