Ligand profile

AGO

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

Bound to: VK055_3692 — ferrous iron transport protein B

Via homolog PDB 3hyt UniProt P33650 Formula C₁₈H₂₂N₇O₁₄P₃
Mol. weight 653.33 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
AGO
PDB
3hyt
UniProt (similar protein)
P33650
Target protein
VK055_3692

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 653.33 Da
LogP (Crippen) -0.65
H-bond donors 8
H-bond acceptors 15
TPSA 316.84 Ų
Rotatable bonds 11
Aromatic rings 3 / 4
Heavy atoms 42
Fraction sp³ C 0.28
Formula C₁₈H₂₂N₇O₁₄P₃

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 316.8
  • −1 ≤ LogP ≤ 5 -0.65
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 653.3
  • LogP ≤ 5 -0.65
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 15
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 316.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CNc1ccccc1C(=O)O[C@@H]2[C@H](O[C@H](C2=O)n3cnc4c3N=C(NC4=O)N)CO[P@@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O
InChI 
InChI=1S/C18H22N7O14P3/c1-20-9-5-3-2-4-8(9)17(28)38-13-10(6-36-42(34,35)39-41(32,33)24-40(29,30)31)37-16(12(13)26)25-7-21-11-14(25)22-18(19)23-15(11)27/h2-5,7,10,13,16,20H,6H2,1H3,(H,34,35)(H3,19,22,23,27)(H4,24,29,30,31,32,33)/t10-,13-,16-/m1/s1
InChIKey 
RVBPPAHXMWBKDD-CKUKBARFSA-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
PF02421

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_3692.

PDB 7

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)