Ligand profile

2GN

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 3zm6 UniProt Q8DNV6 Formula C₂₇H₂₄Cl₂N₈O₄S₂
Mol. weight 659.58 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2GN
PDB
3zm6
UniProt (similar protein)
Q8DNV6
Target protein
KP13_31828

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 659.58 Da
LogP (Crippen) 3.94
H-bond donors 2
H-bond acceptors 10
TPSA 157.20 Ų
Rotatable bonds 7
Aromatic rings 4 / 6
Heavy atoms 43
Fraction sp³ C 0.30
Formula C₂₇H₂₄Cl₂N₈O₄S₂

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 157.2
  • −1 ≤ LogP ≤ 5 3.94
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 659.6
  • LogP ≤ 5 3.94
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 157.2
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)c6n[nH]nn6
InChI 
InChI=1S/C27H24Cl2N8O4S2/c28-21-12-22(29)24(43(39,40)37-7-9-41-10-8-37)11-19(21)26(38)31-27-20(13-30)18-5-6-36(15-23(18)42-27)14-16-1-3-17(4-2-16)25-32-34-35-33-25/h1-4,11-12H,5-10,14-15H2,(H,31,38)(H,32,33,34,35)
InChIKey 
KXJHJZRFLLSTJD-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)