Ligand profile

GPG

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

Bound to: VK055_1879 — ribonuclease T2 family protein

Via homolog PDB 2ea1 UniProt P21338 Formula C₂₀H₂₅N₁₀O₁₂P
Mol. weight 628.45 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GPG
PDB
2ea1
UniProt (similar protein)
P21338
Target protein
VK055_1879

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 628.45 Da
LogP (Crippen) -4.21
H-bond donors 9
H-bond acceptors 19
TPSA 334.32 Ų
Rotatable bonds 8
Aromatic rings 4 / 6
Heavy atoms 43
Fraction sp³ C 0.50
Formula C₂₀H₂₅N₁₀O₁₂P

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 334.3
  • −1 ≤ LogP ≤ 5 -4.21
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 628.5
  • LogP ≤ 5 -4.21
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 19
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 334.3
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[C@@H]4[C@@H]([C@H](O[C@H]4n5cnc6c5N=C(NC6=O)N)CO)O)O)O)N=C(NC2=O)N
InChI 
InChI=1S/C20H25N10O12P/c21-19-25-13-7(15(35)27-19)23-3-29(13)17-11(34)9(32)6(41-17)2-39-43(37,38)42-12-10(33)5(1-31)40-18(12)30-4-24-8-14(30)26-20(22)28-16(8)36/h3-6,9-12,17-18,31-34H,1-2H2,(H,37,38)(H3,21,25,27,35)(H3,22,26,28,36)/t5-,6-,9-,10-,11-,12-,17-,18-/m1/s1
InChIKey 
YYNDAHWXMRBBRC-MHARETSRSA-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
PF00445

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_1879.

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)