Binder profile

ZINC827259

Virtual-screening candidate from ZINC.

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

Via homolog UniProt Q8DNV6 C20H22ClN3O3S2

Tanimoto 0.96

Mol. weight 452.00 Da

Permeability Check

PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID: ZINC827259
UniProt (similar protein): Q8DNV6
Tanimoto: 0.964
Target protein: PA4416

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 452.00 Da

LogP (Crippen) 4.43

H-bond donors 1

H-bond acceptors 5

TPSA 90.27 Å²

Rotatable bonds 6

Aromatic rings 2 / 3

Heavy atoms 29

Fraction sp³ C 0.40

Formula C20H22ClN3O3S2

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 4.43
H-bond donors ≤ 5 1
H-bond acceptors ≤ 10 5

Veber's rules Pass

Rotatable bonds ≤ 10 6
TPSA ≤ 140 Å² 90.3

PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES

CCN(CC)S(=O)(=O)c1ccc(Cl)c(C(=O)Nc2sc3c(c2C#N)CCCC3)c1

InChI

InChI=1S/C20H22ClN3O3S2/c1-3-24(4-2)29(26,27)13-9-10-17(21)15(11-13)19(25)23-20-16(12-22)14-7-5-6-8-18(14)28-20/h9-11H,3-8H2,1-2H3,(H,23,25)

InChIKey

VKXNIAWKFHPGRL-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: 2LG
Homolog: Q8DNV6

External resources

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

ZINC ZINC15 ZINC827259 →
ZINC ZINC20 ZINC827259 →
UniProt UniProt Q8DNV6 (homolog) →
PubChem PubChem (by InChIKey) →
Cheminformatics SwissADME prediction →
Cheminformatics SwissTargetPrediction →
Web Google Scholar (search “ZINC827259”) →

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)