Ligand profile

HBI

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

Bound to: VK055_4932 — GTP cyclohydrolase I

Via homolog PDB 1wpl UniProt P22288 Formula C₉H₁₃N₅O₃
Mol. weight 239.24 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HBI
PDB
1wpl
UniProt (similar protein)
P22288
Target protein
VK055_4932

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 239.24 Da
LogP (Crippen) -1.41
H-bond donors 5
H-bond acceptors 7
TPSA 136.62 Ų
Rotatable bonds 2
Aromatic rings 1 / 2
Heavy atoms 17
Fraction sp³ C 0.44
Formula C₉H₁₃N₅O₃

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 136.6
  • −1 ≤ LogP ≤ 5 -1.41
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 239.2
  • LogP ≤ 5 -1.41
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 136.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]([C@@H](C1=NC2=C(NC1)N=C(NC2=O)N)O)O
InChI 
InChI=1S/C9H13N5O3/c1-3(15)6(16)4-2-11-7-5(12-4)8(17)14-9(10)13-7/h3,6,15-16H,2H2,1H3,(H4,10,11,13,14,17)/t3-,6-/m0/s1
InChIKey 
FEMXZDUTFRTWPE-DZSWIPIPSA-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
PF01227' 'PF06399

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_4932.

PDB 4

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)