Ligand profile

A4P

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

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

Via homolog PDB 1ex8 UniProt P26281 Formula C₁₇H₂₄N₁₀O₁₇P₄
Mol. weight 764.33 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
A4P
PDB
1ex8
UniProt (similar protein)
P26281
Target protein
VK055_2426

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 764.33 Da
LogP (Crippen) -1.62
H-bond donors 10
H-bond acceptors 22
TPSA 410.82 Ų
Rotatable bonds 13
Aromatic rings 3 / 5
Heavy atoms 48
Fraction sp³ C 0.41
Formula C₁₇H₂₄N₁₀O₁₇P₄

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 410.8
  • −1 ≤ LogP ≤ 5 -1.62
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 764.3
  • LogP ≤ 5 -1.62
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 22
Veber's rules Fail
  • Rotatable bonds ≤ 10 13
  • TPSA ≤ 140 Ų 410.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)O[P@@](=O)(O)O[P@@](=O)(O)OCC4=NC5=C(NC4)N=C(NC5=O)N)O)O)N
InChI 
InChI=1S/C17H24N10O17P4/c18-12-8-14(22-4-21-12)27(5-23-8)16-11(29)10(28)7(41-16)3-40-46(33,34)43-48(37,38)44-47(35,36)42-45(31,32)39-2-6-1-20-13-9(24-6)15(30)26-17(19)25-13/h4-5,7,10-11,16,28-29H,1-3H2,(H,31,32)(H,33,34)(H,35,36)(H,37,38)(H2,18,21,22)(H4,19,20,25,26,30)/t7-,10-,11-,16-/m1/s1
InChIKey 
ZKRKFZJAQKKHKL-SUGPNEFASA-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)