Binder profile

ZINC712443

Virtual-screening candidate from ZINC.

Bound to: PA4416 — UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase

Via homolog UniProt Q8DNV6 C20H20ClN3O4S2

Tanimoto 0.75

Mol. weight 465.98 Da

Permeability Check

PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID: ZINC712443
UniProt (similar protein): Q8DNV6
Tanimoto: 0.754
Target protein: PA4416

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 465.98 Da

LogP (Crippen) 3.43

H-bond donors 1

H-bond acceptors 6

TPSA 99.50 Å²

Rotatable bonds 4

Aromatic rings 2 / 4

Heavy atoms 30

Fraction sp³ C 0.40

Formula C20H20ClN3O4S2

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 Å² and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

Lipinski's Rule of Five Pass 0 violations

MW ≤ 500 Da 466.0
LogP ≤ 5 3.43
H-bond donors ≤ 5 1
H-bond acceptors ≤ 10 6

Veber's rules Pass

Rotatable bonds ≤ 10 4
TPSA ≤ 140 Å² 99.5

PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES

N#Cc1c(NC(=O)c2ccc(Cl)c(S(=O)(=O)N3CCOCC3)c2)sc2c1CCCC2

InChI

InChI=1S/C20H20ClN3O4S2/c21-16-6-5-13(11-18(16)30(26,27)24-7-9-28-10-8-24)19(25)23-20-15(12-22)14-3-1-2-4-17(14)29-20/h5-6,11H,1-4,7-10H2,(H,23,25)

InChIKey

XINQJJZPKOSROC-UHFFFAOYSA-N

Provenance

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

Method: LigQ nearest_k
Query: CHEMBL92119
Homolog: Q8DNV6

External resources

Open this ligand in third-party databases and cheminformatics tools.

ZINC ZINC15 ZINC712443 →
ZINC ZINC20 ZINC712443 →
UniProt UniProt Q8DNV6 (homolog) →
PubChem PubChem (by InChIKey) →
Cheminformatics SwissADME prediction →
Cheminformatics SwissTargetPrediction →
Web Google Scholar (search “ZINC712443”) →

Other binders for this protein

Quick navigation to other ligands bound to PA4416.

PDB 9

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

Ligand PDB entry

ChEMBL 9

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)