Ligand profile

HE8

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

Bound to: KP13_02722 — Agmatinase

Via homolog PDB 6q37 UniProt P78540 Formula C₈H₁₈BN₂O₅⁻
Mol. weight 233.05 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HE8
PDB
6q37
UniProt (similar protein)
P78540
Target protein
KP13_02722

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 233.05 Da
LogP (Crippen) -2.32
H-bond donors 6
H-bond acceptors 6
TPSA 136.04 Ų
Rotatable bonds 5
Aromatic rings 0 / 1
Heavy atoms 16
Fraction sp³ C 0.88
Formula C₈H₁₈BN₂O₅⁻

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 136.0
  • −1 ≤ LogP ≤ 5 -2.32
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 233.1
  • LogP ≤ 5 -2.32
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 136.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[B-](CCC[C@H]1CNC[C@]1(C(=O)O)N)(O)(O)O
InChI 
InChI=1S/C8H18BN2O5/c10-8(7(12)13)5-11-4-6(8)2-1-3-9(14,15)16/h6,11,14-16H,1-5,10H2,(H,12,13)/q-1/t6-,8-/m0/s1
InChIKey 
JNNZQSJBRFVUJB-XPUUQOCRSA-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
PF00491

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_02722.

PDB 11

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 100

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)