Ligand profile

IGM

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 3zm5 UniProt Q8DNV6 Formula 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
KP13_31828

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.

  • TPSA ≤ 90 Ų 123.0
  • −1 ≤ LogP ≤ 5 4.46
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 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)