Binder profile

CHEMBL93913

Bioactivity hit from ChEMBL on a similar protein.

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

Via homolog UniProt Q8DNV6 C26H25Cl2N3O4S2

pchembl 7.17 ~67.6 nM

Mol. weight 578.54 Da

Permeability Check

PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID: CHEMBL93913
UniProt (similar protein): Q8DNV6
pchembl: 7.170 (~67.6 nM)
Target protein: PA4416

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 578.54 Da

LogP (Crippen) 6.19

H-bond donors 2

H-bond acceptors 6

TPSA 110.50 Å²

Rotatable bonds 7

Aromatic rings 3 / 4

Heavy atoms 37

Fraction sp³ C 0.31

Formula C26H25Cl2N3O4S2

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 578.5
LogP ≤ 5 6.19
H-bond donors ≤ 5 2
H-bond acceptors ≤ 10 6

Veber's rules Pass

Rotatable bonds ≤ 10 7
TPSA ≤ 140 Å² 110.5

PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES

CCN(CC)S(=O)(=O)c1cc(C(=O)Nc2sc3c(c2C#N)CCC(c2ccc(O)cc2)C3)c(Cl)cc1Cl

InChI

InChI=1S/C26H25Cl2N3O4S2/c1-3-31(4-2)37(34,35)24-12-19(21(27)13-22(24)28)25(33)30-26-20(14-29)18-10-7-16(11-23(18)36-26)15-5-8-17(32)9-6-15/h5-6,8-9,12-13,16,32H,3-4,7,10-11H2,1-2H3,(H,30,33)

InChIKey

UMCBFQNRSMSXAY-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 CHEMBL93913 →
UniProt UniProt Q8DNV6 (homolog) →
PubChem PubChem (by InChIKey) →
Cheminformatics SwissADME prediction →
Cheminformatics SwissTargetPrediction →
Web Google Scholar (search “CHEMBL93913”) →

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)