Ligand profile

GDD

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

Bound to: VK055_4026 — ADP-ribose pyrophosphatase

Via homolog PDB 3o61 UniProt P37128 Formula C₁₆H₂₅N₅O₁₆P₂
Mol. weight 605.34 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GDD
PDB
3o61
UniProt (similar protein)
P37128
Target protein
VK055_4026

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 605.34 Da
LogP (Crippen) -4.63
H-bond donors 10
H-bond acceptors 18
TPSA 331.72 Ų
Rotatable bonds 9
Aromatic rings 2 / 4
Heavy atoms 39
Fraction sp³ C 0.69
Formula C₁₆H₂₅N₅O₁₆P₂

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 331.7
  • −1 ≤ LogP ≤ 5 -4.63
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 605.3
  • LogP ≤ 5 -4.63
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 18
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 331.7
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)O[P@](=O)(O)O[C@@H]4[C@H]([C@H]([C@@H]([C@H](O4)CO)O)O)O)O)O)N=C(NC2=O)N
InChI 
InChI=1S/C16H25N5O16P2/c17-16-19-12-6(13(28)20-16)18-3-21(12)14-10(26)8(24)5(34-14)2-33-38(29,30)37-39(31,32)36-15-11(27)9(25)7(23)4(1-22)35-15/h3-5,7-11,14-15,22-27H,1-2H2,(H,29,30)(H,31,32)(H3,17,19,20,28)/t4-,5-,7-,8-,9+,10-,11+,14-,15-/m1/s1
InChIKey 
MVMSCBBUIHUTGJ-GDJBGNAASA-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)