Binder profile

CHEMBL329389

Bioactivity hit from ChEMBL on a similar protein.

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

Via homolog UniProt Q8DNV6 C26H23Cl2N3O4S2

pchembl 7.16 ~69.2 nM

Mol. weight 576.53 Da

Permeability Check

PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID: CHEMBL329389
UniProt (similar protein): Q8DNV6
pchembl: 7.160 (~69.2 nM)
Target protein: PA4416

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 576.53 Da

LogP (Crippen) 5.47

H-bond donors 1

H-bond acceptors 6

TPSA 99.50 Å²

Rotatable bonds 5

Aromatic rings 3 / 5

Heavy atoms 37

Fraction sp³ C 0.31

Formula C26H23Cl2N3O4S2

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 Fail 2 violations

MW ≤ 500 Da 576.5
LogP ≤ 5 5.47
H-bond donors ≤ 5 1
H-bond acceptors ≤ 10 6

Veber's rules Pass

Rotatable bonds ≤ 10 5
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)c(Cl)cc2Cl)sc2c1CCC(c1ccccc1)C2

InChI

InChI=1S/C26H23Cl2N3O4S2/c27-21-14-22(28)24(37(33,34)31-8-10-35-11-9-31)13-19(21)25(32)30-26-20(15-29)18-7-6-17(12-23(18)36-26)16-4-2-1-3-5-16/h1-5,13-14,17H,6-12H2,(H,30,32)

InChIKey

RFBHGTAROUPZGA-UHFFFAOYSA-N

Provenance

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

Method: LigQ nearest_k
Source: ChEMBL
Curation: pdb_similarity_tanimoto
Binding sites: PF01225' 'PF02875' 'PF08245

External resources

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

ChEMBL ChEMBL compound CHEMBL329389 →
UniProt UniProt Q8DNV6 (homolog) →
PubChem PubChem (by InChIKey) →
Cheminformatics SwissADME prediction →
Cheminformatics SwissTargetPrediction →
Web Google Scholar (search “CHEMBL329389”) →

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 8

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)