Ligand profile

BGO

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

Bound to: KP13_00684 — Ferrous iron transport protein B

Via homolog PDB 3tah UniProt Q5M586 Formula C₁₈H₂₂N₆O₁₂P₂
Mol. weight 576.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
BGO
PDB
3tah
UniProt (similar protein)
Q5M586
Target protein
KP13_00684

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 576.35 Da
LogP (Crippen) -0.55
H-bond donors 7
H-bond acceptors 14
TPSA 270.67 Ų
Rotatable bonds 9
Aromatic rings 3 / 4
Heavy atoms 38
Fraction sp³ C 0.33
Formula C₁₈H₂₂N₆O₁₂P₂

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 270.7
  • −1 ≤ LogP ≤ 5 -0.55
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 576.4
  • LogP ≤ 5 -0.55
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 270.7
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]([C@@H]2O)n3cnc4c3N=C(NC4=O)N)CO[P@](=O)(O)OP(=O)(O)O
InChI 
InChI=1S/C18H22N6O12P2/c1-20-9-5-3-2-4-8(9)17(27)35-13-10(6-33-38(31,32)36-37(28,29)30)34-16(12(13)25)24-7-21-11-14(24)22-18(19)23-15(11)26/h2-5,7,10,12-13,16,20,25H,6H2,1H3,(H,31,32)(H2,28,29,30)(H3,19,22,23,26)/t10-,12-,13-,16-/m1/s1
InChIKey 
DAJQUPOUYBWRQQ-XNIJJKJLSA-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' 'PF17910

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_00684.

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)