Ligand profile

GAV

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

Bound to: VK055_0696 — diguanylate cyclase domain protein

Via homolog PDB 2v0n UniProt B8GZM2 Formula C₁₀H₁₆N₅O₁₃P₃S
Mol. weight 539.25 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GAV
PDB
2v0n
UniProt (similar protein)
B8GZM2
Target protein
VK055_0696

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 539.25 Da
LogP (Crippen) -1.40
H-bond donors 8
H-bond acceptors 14
TPSA 278.87 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 32
Fraction sp³ C 0.50
Formula C₁₀H₁₆N₅O₁₃P₃S

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 278.9
  • −1 ≤ LogP ≤ 5 -1.40
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 539.2
  • LogP ≤ 5 -1.40
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 278.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O[P@@](=O)(O)OP(=O)(O)O)S)O)O)N=C(NC2=O)N
InChI 
InChI=1S/C10H16N5O13P3S/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(26-9)1-25-31(24,32)28-30(22,23)27-29(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,32)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-,31-/m1/s1
InChIKey 
YRUWXBKVSXSSGS-KIOICMOXSA-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
PF00990

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_0696.

PDB 2

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)