Ligand profile

5RY

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

Bound to: VK055_2426 — 2-amino-4-hydroxy-6- hydroxymethyldihydropteridine diphosphokinase

Via homolog PDB 5ett UniProt Q2G0Q5 Formula C₁₃H₉FN₆OS
Mol. weight 316.32 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5RY
PDB
5ett
UniProt (similar protein)
Q2G0Q5
Target protein
VK055_2426

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 316.32 Da
LogP (Crippen) 1.53
H-bond donors 3
H-bond acceptors 6
TPSA 124.24 Ų
Rotatable bonds 3
Aromatic rings 3 / 3
Heavy atoms 22
Fraction sp³ C 0.08
Formula C₁₃H₉FN₆OS

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 124.2
  • −1 ≤ LogP ≤ 5 1.53
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 316.3
  • LogP ≤ 5 1.53
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 124.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(c(cc1C#N)F)CSc2[nH]c3c(n2)C(=O)NC(=N3)N
InChI 
InChI=1S/C13H9FN6OS/c14-8-3-6(4-15)1-2-7(8)5-22-13-17-9-10(19-13)18-12(16)20-11(9)21/h1-3H,5H2,(H4,16,17,18,19,20,21)
InChIKey 
GEUVDHJEINQZML-UHFFFAOYSA-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
PF01288

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_2426.

PDB 27

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

Ligand PDB entry

ChEMBL 21

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)