Ligand profile

J1A

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

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

Via homolog PDB 3ud5 UniProt P26281 Formula C₂₄H₃₂N₁₂O₄S
Mol. weight 584.67 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
J1A
PDB
3ud5
UniProt (similar protein)
P26281
Target protein
VK055_2426

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 584.67 Da
LogP (Crippen) -1.38
H-bond donors 6
H-bond acceptors 16
TPSA 232.13 Ų
Rotatable bonds 9
Aromatic rings 4 / 6
Heavy atoms 41
Fraction sp³ C 0.54
Formula C₂₄H₃₂N₁₂O₄S

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 232.1
  • −1 ≤ LogP ≤ 5 -1.38
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 584.7
  • LogP ≤ 5 -1.38
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 16
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 232.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c(nc2c(n1)N=C(NC2=O)N)CNCCN3CCC(CC3)SC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O
InChI 
InChI=1S/C24H32N12O4S/c25-19-15-21(30-10-29-19)36(11-31-15)23-18(38)17(37)14(40-23)9-41-13-1-4-35(5-2-13)6-3-27-7-12-8-28-20-16(32-12)22(39)34-24(26)33-20/h8,10-11,13-14,17-18,23,27,37-38H,1-7,9H2,(H2,25,29,30)(H3,26,28,33,34,39)/t14-,17-,18-,23-/m1/s1
InChIKey 
KWIHONXLDHOYOZ-YMYXXHFHSA-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)