Ligand profile

XAH

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

Bound to: KP13_02199 — Lysyl-tRNA synthetase

Via homolog PDB 3e9i UniProt Q9RHV9 Formula C₁₆H₂₇N₈O₈P
Mol. weight 490.41 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
XAH
PDB
3e9i
UniProt (similar protein)
Q9RHV9
Target protein
KP13_02199

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 490.41 Da
LogP (Crippen) -2.35
H-bond donors 7
H-bond acceptors 14
TPSA 256.21 Ų
Rotatable bonds 11
Aromatic rings 2 / 3
Heavy atoms 33
Fraction sp³ C 0.62
Formula C₁₆H₂₇N₈O₈P

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 256.2
  • −1 ≤ LogP ≤ 5 -2.35
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 490.4
  • LogP ≤ 5 -2.35
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 256.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)ONC(=O)[C@H](CCCCN)N)O)O)N
InChI 
InChI=1S/C16H27N8O8P/c17-4-2-1-3-8(18)15(27)23-32-33(28,29)30-5-9-11(25)12(26)16(31-9)24-7-22-10-13(19)20-6-21-14(10)24/h6-9,11-12,16,25-26H,1-5,17-18H2,(H,23,27)(H,28,29)(H2,19,20,21)/t8-,9+,11+,12+,16+/m0/s1
InChIKey 
UZJSLDPAROCUBS-LEJQEAHTSA-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
PF00152

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_02199.

PDB 17

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

Ligand PDB entry

ChEMBL 2

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)