Ligand profile

J1I

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

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

Via homolog PDB 6an6 UniProt P26281 Formula C₂₄H₃₅N₁₂O₈PS
Mol. weight 682.66 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
J1I
PDB
6an6
UniProt (similar protein)
P26281
Target protein
VK055_2426

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 682.66 Da
LogP (Crippen) -2.04
H-bond donors 9
H-bond acceptors 17
TPSA 305.34 Ų
Rotatable bonds 12
Aromatic rings 3 / 5
Heavy atoms 46
Fraction sp³ C 0.54
Formula C₂₄H₃₅N₁₂O₈PS

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 305.3
  • −1 ≤ LogP ≤ 5 -2.04
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 682.7
  • LogP ≤ 5 -2.04
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 17
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 305.3
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)NCCN(CCSC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)CP(=O)(O)O)C
InChI 
InChI=1S/C24H35N12O8PS/c1-24(2)16(31-13-18(34-24)32-23(26)33-20(13)39)21(40)27-3-4-35(10-45(41,42)43)5-6-46-7-11-14(37)15(38)22(44-11)36-9-30-12-17(25)28-8-29-19(12)36/h8-9,11,14-15,22,37-38H,3-7,10H2,1-2H3,(H,27,40)(H2,25,28,29)(H2,41,42,43)(H4,26,32,33,34,39)/t11-,14-,15-,22-/m1/s1
InChIKey 
LNONYTMYGAJODO-HUYKWJOFSA-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)