Ligand profile

1LG

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

Bound to: KP13_31828 — UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase

Via homolog PDB 2am1 UniProt Q8DNV6 Formula C₂₀H₁₉Cl₂N₃O₄S₂
Mol. weight 500.43 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1LG
PDB
2am1
UniProt (similar protein)
Q8DNV6
Target protein
KP13_31828

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 500.43 Da
LogP (Crippen) 4.08
H-bond donors 1
H-bond acceptors 6
TPSA 99.50 Ų
Rotatable bonds 4
Aromatic rings 2 / 4
Heavy atoms 31
Fraction sp³ C 0.40
Formula C₂₀H₁₉Cl₂N₃O₄S₂

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.

  • TPSA ≤ 90 Ų 99.5
  • −1 ≤ LogP ≤ 5 4.08
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 500.4
  • LogP ≤ 5 4.08
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 99.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c(c(cc(c1S(=O)(=O)N2CCOCC2)Cl)Cl)C(=O)Nc3c(c4c(s3)CCCC4)C#N
InChI 
InChI=1S/C20H19Cl2N3O4S2/c21-15-10-16(22)18(31(27,28)25-5-7-29-8-6-25)9-13(15)19(26)24-20-14(11-23)12-3-1-2-4-17(12)30-20/h9-10H,1-8H2,(H,24,26)
InChIKey 
JMCVGASJAJMFPN-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target 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 ligands for this protein

Quick navigation to other ligands bound to KP13_31828.

PDB 17

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)