Binder profile

IGM

Ligand co-crystallized with a similar protein (Protein Data Bank).

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

Via homolog PDB 3zm5 UniProt Q8DNV6 C26H24Cl2N4O5S2
Mol. weight 607.54 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
IGM
PDB
3zm5
UniProt (similar protein)
Q8DNV6
Target protein
PA4416

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 607.54 Da
LogP (Crippen) 4.46
H-bond donors 2
H-bond acceptors 8
TPSA 122.97 Ų
Rotatable bonds 6
Aromatic rings 3 / 5
Heavy atoms 39
Fraction sp³ C 0.31
Formula C26H24Cl2N4O5S2

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 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 607.5
  • LogP ≤ 5 4.46
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 123.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1CN2CCc3c(sc(c3C#N)NC(=O)c4cc(c(cc4Cl)Cl)S(=O)(=O)N5CCOCC5)C2)O
InChI 
InChI=1S/C26H24Cl2N4O5S2/c27-21-12-22(28)24(39(35,36)32-7-9-37-10-8-32)11-19(21)25(34)30-26-20(13-29)18-5-6-31(15-23(18)38-26)14-16-1-3-17(33)4-2-16/h1-4,11-12,33H,5-10,14-15H2,(H,30,34)
InChIKey 
VSLIZFRORGVSOU-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
PDB
Binding sites
PF01225' 'PF02875' 'PF08245

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA4416.

PDB 8

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 50

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

Compound Similarity (Tanimoto)