Binder profile

ZINC1433755

Virtual-screening candidate from ZINC.

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

Via homolog UniProt Q8DNV6 C19H18ClN3O4S2

Tanimoto 0.78

Mol. weight 451.96 Da

Permeability Check

PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID: ZINC1433755
UniProt (similar protein): Q8DNV6
Tanimoto: 0.781
Target protein: PA4416

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 451.96 Da

LogP (Crippen) 3.04

H-bond donors 1

H-bond acceptors 6

TPSA 99.50 Å²

Rotatable bonds 4

Aromatic rings 2 / 4

Heavy atoms 29

Fraction sp³ C 0.37

Formula C19H18ClN3O4S2

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 452.0
LogP ≤ 5 3.04
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)c2cc(S(=O)(=O)N3CCOCC3)ccc2Cl)sc2c1CCC2

InChI

InChI=1S/C19H18ClN3O4S2/c20-16-5-4-12(29(25,26)23-6-8-27-9-7-23)10-14(16)18(24)22-19-15(11-21)13-2-1-3-17(13)28-19/h4-5,10H,1-3,6-9H2,(H,22,24)

InChIKey

GRPMFEOVLFSTAJ-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 ZINC1433755 →
ZINC ZINC20 ZINC1433755 →
UniProt UniProt Q8DNV6 (homolog) →
PubChem PubChem (by InChIKey) →
Cheminformatics SwissADME prediction →
Cheminformatics SwissTargetPrediction →
Web Google Scholar (search “ZINC1433755”) →

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)