Ligand profile

ZINC3920510

Virtual-screening candidate from ZINC.

Bound to: KP13_05440 — Peptide transport periplasmic protein sapA

Via homolog UniProt B8F653 Formula C₁₄H₂₁N₃O₁₀S
Tanimoto 0.75
Mol. weight 423.40 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC3920510
UniProt (similar protein)
B8F653
Tanimoto
0.750
Target protein
KP13_05440

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 423.40 Da
LogP (Crippen) -2.47
H-bond donors 7
H-bond acceptors 8
TPSA 233.42 Ų
Rotatable bonds 14
Aromatic rings 0 / 0
Heavy atoms 28
Fraction sp³ C 0.57
Formula C₁₄H₂₁N₃O₁₀S

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 233.4
  • −1 ≤ LogP ≤ 5 -2.47
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 423.4
  • LogP ≤ 5 -2.47
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 14
  • TPSA ≤ 140 Ų 233.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
N[C@@H](CCC(=O)N[C@@H](CS[C@@H](CC(=O)O)C(=O)O)C(=O)NCC(=O)O)C(=O)O
InChI 
InChI=1S/C14H21N3O10S/c15-6(13(24)25)1-2-9(18)17-7(12(23)16-4-11(21)22)5-28-8(14(26)27)3-10(19)20/h6-8H,1-5,15H2,(H,16,23)(H,17,18)(H,19,20)(H,21,22)(H,24,25)(H,26,27)/t6-,7-,8-/m0/s1
InChIKey 
PWCIUOASSAHGHI-FXQIFTODSA-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)