Ligand profile

ZINC4556756

Virtual-screening candidate from ZINC.

Bound to: KP13_05440 — Peptide transport periplasmic protein sapA

Via homolog UniProt B8F653 Formula C₁₃H₁₉N₃O₈S
Tanimoto 0.73
Mol. weight 377.38 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC4556756
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 377.38 Da
LogP (Crippen) -2.29
H-bond donors 5
H-bond acceptors 8
TPSA 192.96 Ų
Rotatable bonds 11
Aromatic rings 0 / 0
Heavy atoms 25
Fraction sp³ C 0.54
Formula C₁₃H₁₉N₃O₈S

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 193.0
  • −1 ≤ LogP ≤ 5 -2.29
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 377.4
  • LogP ≤ 5 -2.29
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 193.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)C(=O)SC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=O)O
InChI 
InChI=1S/C13H19N3O8S/c1-6(17)13(24)25-5-8(11(21)15-4-10(19)20)16-9(18)3-2-7(14)12(22)23/h7-8H,2-5,14H2,1H3,(H,15,21)(H,16,18)(H,19,20)(H,22,23)/t7-,8-/m0/s1
InChIKey 
PPLZFKVEEDKGDM-YUMQZZPRSA-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)