Ligand profile

J1C

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

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

Via homolog PDB 3udv UniProt P26281 Formula C₂₆H₃₆N₁₂O₅S
Mol. weight 628.72 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
J1C
PDB
3udv
UniProt (similar protein)
P26281
Target protein
VK055_2426

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 628.72 Da
LogP (Crippen) -1.02
H-bond donors 7
H-bond acceptors 16
TPSA 247.81 Ų
Rotatable bonds 8
Aromatic rings 3 / 6
Heavy atoms 44
Fraction sp³ C 0.58
Formula C₂₆H₃₆N₁₂O₅S

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 247.8
  • −1 ≤ LogP ≤ 5 -1.02
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 628.7
  • LogP ≤ 5 -1.02
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 16
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 247.8
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)C(=O)NCCN3CCC(CC3)SC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)C
InChI 
InChI=1S/C26H36N12O5S/c1-26(2)18(33-15-20(36-26)34-25(28)35-22(15)41)23(42)29-5-8-37-6-3-12(4-7-37)44-9-13-16(39)17(40)24(43-13)38-11-32-14-19(27)30-10-31-21(14)38/h10-13,16-17,24,39-40H,3-9H2,1-2H3,(H,29,42)(H2,27,30,31)(H4,28,34,35,36,41)/t13-,16-,17-,24-/m1/s1
InChIKey 
LXHMIPYFQUZUMS-FUKGTJLDSA-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)