Binder profile

ZINC4070250

Virtual-screening candidate from ZINC.

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

Via homolog UniProt Q8DNV6 C20H23N3O3S2

Tanimoto 0.75

Mol. weight 417.56 Da

Permeability Check

PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID: ZINC4070250
UniProt (similar protein): Q8DNV6
Tanimoto: 0.750
Target protein: PA4416

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 417.56 Da

LogP (Crippen) 3.78

H-bond donors 1

H-bond acceptors 5

TPSA 90.27 Å²

Rotatable bonds 6

Aromatic rings 2 / 3

Heavy atoms 28

Fraction sp³ C 0.40

Formula C20H23N3O3S2

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 417.6
LogP ≤ 5 3.78
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(C(=O)Nc2sc3c(c2C#N)CCCC3)cc1

InChI

InChI=1S/C20H23N3O3S2/c1-3-23(4-2)28(25,26)15-11-9-14(10-12-15)19(24)22-20-17(13-21)16-7-5-6-8-18(16)27-20/h9-12H,3-8H2,1-2H3,(H,22,24)

InChIKey

VWYWYXTYZNEEBS-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 ZINC4070250 →
ZINC ZINC20 ZINC4070250 →
UniProt UniProt Q8DNV6 (homolog) →
PubChem PubChem (by InChIKey) →
Cheminformatics SwissADME prediction →
Cheminformatics SwissTargetPrediction →
Web Google Scholar (search “ZINC4070250”) →

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)