Ligand profile

AMO

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

Bound to: KP13_04176 — Asparaginyl-tRNA synthetase

Via homolog PDB 3nem UniProt Q52428 Formula C₁₄H₁₉N₆O₁₀P
Mol. weight 462.31 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
AMO
PDB
3nem
UniProt (similar protein)
Q52428
Target protein
KP13_04176

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 462.31 Da
LogP (Crippen) -2.51
H-bond donors 6
H-bond acceptors 14
TPSA 255.46 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 31
Fraction sp³ C 0.50
Formula C₁₄H₁₉N₆O₁₀P

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 255.5
  • −1 ≤ LogP ≤ 5 -2.51
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 462.3
  • LogP ≤ 5 -2.51
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 255.5
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)OC(=O)[C@H](CC(=O)O)N)O)O)N
InChI 
InChI=1S/C14H19N6O10P/c15-5(1-7(21)22)14(25)30-31(26,27)28-2-6-9(23)10(24)13(29-6)20-4-19-8-11(16)17-3-18-12(8)20/h3-6,9-10,13,23-24H,1-2,15H2,(H,21,22)(H,26,27)(H2,16,17,18)/t5-,6+,9+,10+,13+/m0/s1
InChIKey 
QPBSGQWTJLPZNF-VWJPMABRSA-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_04176.

PDB 4

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

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)