Ligand profile

87Y

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

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

Via homolog PDB 1dy3 UniProt P26281 Formula C₁₆H₁₉N₅O₂
Mol. weight 313.36 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
87Y
PDB
1dy3
UniProt (similar protein)
P26281
Target protein
VK055_2426

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 313.36 Da
LogP (Crippen) 1.23
H-bond donors 4
H-bond acceptors 6
TPSA 116.39 Ų
Rotatable bonds 4
Aromatic rings 2 / 3
Heavy atoms 23
Fraction sp³ C 0.31
Formula C₁₆H₁₉N₅O₂

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 1.23
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 313.4
  • LogP ≤ 5 1.23
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 116.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@]1(C(=NC2=C(N1)N=C(NC2=O)N)CO)CCc3ccccc3
InChI 
InChI=1S/C16H19N5O2/c1-16(8-7-10-5-3-2-4-6-10)11(9-22)18-12-13(21-16)19-15(17)20-14(12)23/h2-6,22H,7-9H2,1H3,(H4,17,19,20,21,23)/t16-/m0/s1
InChIKey 
XMFJTCGUDFSWSW-INIZCTEOSA-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)