Ligand profile

AYL

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

Bound to: VK055_0128 — fadD

Via homolog PDB 3ni2 UniProt Q941M3 Formula C₁₉H₂₄N₅O₈P
Mol. weight 481.40 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
AYL
PDB
3ni2
UniProt (similar protein)
Q941M3
Target protein
VK055_0128

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 481.40 Da
LogP (Crippen) 0.50
H-bond donors 5
H-bond acceptors 12
TPSA 195.30 Ų
Rotatable bonds 9
Aromatic rings 3 / 4
Heavy atoms 33
Fraction sp³ C 0.42
Formula C₁₉H₂₄N₅O₈P

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 195.3
  • −1 ≤ LogP ≤ 5 0.50
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 481.4
  • LogP ≤ 5 0.50
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 195.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1CCCO[P@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)O
InChI 
InChI=1S/C19H24N5O8P/c20-17-14-18(22-9-21-17)24(10-23-14)19-16(27)15(26)13(32-19)8-31-33(28,29)30-7-1-2-11-3-5-12(25)6-4-11/h3-6,9-10,13,15-16,19,25-27H,1-2,7-8H2,(H,28,29)(H2,20,21,22)/t13-,15-,16-,19-/m1/s1
InChIKey 
AWKHKUUJFJBBRQ-NVQRDWNXSA-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
PF00501

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_0128.

PDB 9

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)