Ligand profile

ADV

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

Bound to: VK055_4026 — ADP-ribose pyrophosphatase

Via homolog PDB 1khz UniProt Q93K97 Formula C₁₆H₂₅N₅O₁₃P₂
Mol. weight 557.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ADV
PDB
1khz
UniProt (similar protein)
Q93K97
Target protein
VK055_4026

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 557.35 Da
LogP (Crippen) -3.17
H-bond donors 8
H-bond acceptors 16
TPSA 282.29 Ų
Rotatable bonds 9
Aromatic rings 2 / 4
Heavy atoms 36
Fraction sp³ C 0.69
Formula C₁₆H₂₅N₅O₁₃P₂

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 282.3
  • −1 ≤ LogP ≤ 5 -3.17
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 557.3
  • LogP ≤ 5 -3.17
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 16
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 282.3
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)(C[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@H](O4)O)O)O)O)O)O)N
InChI 
InChI=1S/C16H25N5O13P2/c17-13-8-14(19-3-18-13)21(4-20-8)15-11(24)9(22)6(33-15)1-31-35(27,28)5-36(29,30)32-2-7-10(23)12(25)16(26)34-7/h3-4,6-7,9-12,15-16,22-26H,1-2,5H2,(H,27,28)(H,29,30)(H2,17,18,19)/t6-,7-,9-,10-,11-,12-,15-,16+/m1/s1
InChIKey 
ZPZRETFSCSWNDT-DBXCYWGHSA-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
PF00293

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_4026.

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)