Ligand profile

XA1

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

Bound to: KP13_02722 — Agmatinase

Via homolog PDB 4ixv UniProt P78540 Formula C₁₈H₂₉BClN₂O₅⁻
Mol. weight 399.70 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
XA1
PDB
4ixv
UniProt (similar protein)
P78540
Target protein
KP13_02722

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 399.70 Da
LogP (Crippen) 1.42
H-bond donors 5
H-bond acceptors 6
TPSA 127.25 Ų
Rotatable bonds 9
Aromatic rings 1 / 2
Heavy atoms 27
Fraction sp³ C 0.61
Formula C₁₈H₂₉BClN₂O₅⁻

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 127.3
  • −1 ≤ LogP ≤ 5 1.42
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 399.7
  • LogP ≤ 5 1.42
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 127.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[B-](CCCC[C@@](C1CCN(CC1)Cc2ccc(cc2)Cl)(C(=O)O)N)(O)(O)O
InChI 
InChI=1S/C18H29BClN2O5/c20-16-5-3-14(4-6-16)13-22-11-7-15(8-12-22)18(21,17(23)24)9-1-2-10-19(25,26)27/h3-6,15,25-27H,1-2,7-13,21H2,(H,23,24)/q-1/t18-/m1/s1
InChIKey 
ZRLSZURFUKVIRB-GOSISDBHSA-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)