Binder profile

XAH

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

Bound to: PA3700 — lysine--tRNA ligase

Via homolog PDB 3e9i UniProt Q9RHV9 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
PA3700

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.

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 TPW 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 binders for this protein

Quick navigation to other ligands bound to PA3700.

PDB 16

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)