Ligand profile

AYD

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

Bound to: VK055_2490 — acetolactate synthase, large subunit, biosynthetic type

Via homolog PDB 1n0h UniProt P07342 Formula C₁₁H₂₀N₄O₇P₂
Mol. weight 382.25 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
AYD
PDB
1n0h
UniProt (similar protein)
P07342
Target protein
VK055_2490

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 382.25 Da
LogP (Crippen) 0.98
H-bond donors 5
H-bond acceptors 8
TPSA 177.12 Ų
Rotatable bonds 9
Aromatic rings 1 / 1
Heavy atoms 24
Fraction sp³ C 0.45
Formula C₁₁H₂₀N₄O₇P₂

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 177.1
  • −1 ≤ LogP ≤ 5 0.98
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 382.3
  • LogP ≤ 5 0.98
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 177.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ncc(c(n1)N)CN/C(=C/CCO[P@@](=O)(O)OP(=O)(O)O)/C
InChI 
InChI=1S/C11H20N4O7P2/c1-8(13-6-10-7-14-9(2)15-11(10)12)4-3-5-21-24(19,20)22-23(16,17)18/h4,7,13H,3,5-6H2,1-2H3,(H,19,20)(H2,12,14,15)(H2,16,17,18)/b8-4+
InChIKey 
DPGNBHAKLFOOJK-XBXARRHUSA-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
PF02775' 'PF02776

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_2490.

PDB 36

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

Ligand PDB entry

ChEMBL 36

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)