Ligand profile

5AL

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

Bound to: VK055_4487 — alanine--tRNA ligase

Via homolog PDB 3hxy UniProt P00957 Formula C₁₃H₁₉N₆O₈P
Mol. weight 418.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5AL
PDB
3hxy
UniProt (similar protein)
P00957
Target protein
VK055_4487

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 418.30 Da
LogP (Crippen) -1.96
H-bond donors 5
H-bond acceptors 13
TPSA 218.16 Ų
Rotatable bonds 6
Aromatic rings 2 / 3
Heavy atoms 28
Fraction sp³ C 0.54
Formula C₁₃H₁₉N₆O₈P

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 218.2
  • −1 ≤ LogP ≤ 5 -1.96
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 418.3
  • LogP ≤ 5 -1.96
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 218.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H](C(=O)O[P@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)N
InChI 
InChI=1S/C13H19N6O8P/c1-5(14)13(22)27-28(23,24)25-2-6-8(20)9(21)12(26-6)19-4-18-7-10(15)16-3-17-11(7)19/h3-6,8-9,12,20-21H,2,14H2,1H3,(H,23,24)(H2,15,16,17)/t5-,6+,8+,9+,12+/m0/s1
InChIKey 
ISYFCRWDMNBLTM-MACXSXHHSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF01411

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_4487.

PDB 6

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)