Ligand profile

X8A

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

Bound to: KP13_02722 — Agmatinase

Via homolog PDB 4i06 UniProt P78540 Formula C₁₄H₃₀BN₂O₅⁻
Mol. weight 317.21 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
X8A
PDB
4i06
UniProt (similar protein)
P78540
Target protein
KP13_02722

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 317.21 Da
LogP (Crippen) -0.01
H-bond donors 5
H-bond acceptors 6
TPSA 113.26 Ų
Rotatable bonds 10
Aromatic rings 0 / 1
Heavy atoms 22
Fraction sp³ C 0.93
Formula C₁₄H₃₀BN₂O₅⁻

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 113.3
  • −1 ≤ LogP ≤ 5 -0.01
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 317.2
  • LogP ≤ 5 -0.01
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 113.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[B-](CCCC[C@@](CCN1CCCCC1)(C(=O)O)NC)(O)(O)O
InChI 
InChI=1S/C14H30BN2O5/c1-16-14(13(18)19,7-3-4-9-15(20,21)22)8-12-17-10-5-2-6-11-17/h16,20-22H,2-12H2,1H3,(H,18,19)/q-1/t14-/m1/s1
InChIKey 
XUSDRKPOXSYXRQ-CQSZACIVSA-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)