Ligand profile

ROI

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

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

Via homolog PDB 1cbk UniProt P43777 Formula C₈H₁₁N₅O₂
Mol. weight 209.21 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ROI
PDB
1cbk
UniProt (similar protein)
P43777
Target protein
VK055_2426

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 209.21 Da
LogP (Crippen) 0.14
H-bond donors 4
H-bond acceptors 5
TPSA 116.39 Ų
Rotatable bonds 0
Aromatic rings 1 / 2
Heavy atoms 15
Fraction sp³ C 0.38
Formula C₈H₁₁N₅O₂

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 116.4
  • −1 ≤ LogP ≤ 5 0.14
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 209.2
  • LogP ≤ 5 0.14
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 116.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1(C(=NC2=C(N1)N=C(NC2=O)N)O)C
InChI 
InChI=1S/C8H11N5O2/c1-8(2)6(15)10-3-4(13-8)11-7(9)12-5(3)14/h1-2H3,(H,10,15)(H4,9,11,12,13,14)
InChIKey 
JMLQSLXEUWNWFI-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)