Ligand profile

1EE

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

Bound to: KP13_02722 — Agmatinase

Via homolog PDB 4ie3 UniProt P78540 Formula C₁₃H₂₈BN₂O₆⁻
Mol. weight 319.19 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1EE
PDB
4ie3
UniProt (similar protein)
P78540
Target protein
KP13_02722

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 319.19 Da
LogP (Crippen) -1.30
H-bond donors 6
H-bond acceptors 7
TPSA 147.48 Ų
Rotatable bonds 9
Aromatic rings 0 / 1
Heavy atoms 22
Fraction sp³ C 0.92
Formula C₁₃H₂₈BN₂O₆⁻

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 147.5
  • −1 ≤ LogP ≤ 5 -1.30
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 319.2
  • LogP ≤ 5 -1.30
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 147.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[B-](CCCC[C@@](CCN1CCC(CC1)O)(C(=O)O)N)(O)(O)O
InChI 
InChI=1S/C13H28BN2O6/c15-13(12(18)19,5-1-2-7-14(20,21)22)6-10-16-8-3-11(17)4-9-16/h11,17,20-22H,1-10,15H2,(H,18,19)/q-1/t13-/m1/s1
InChIKey 
BEHPULZVRPBIEQ-CYBMUJFWSA-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)