Ligand profile

AIF

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

Bound to: KP13_02046 — Riboflavin biosynthesis bifunctional protein ribD

Via homolog PDB 3ex8 UniProt P17618 Formula C₉H₁₅N₄O₉P
Mol. weight 354.21 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
AIF
PDB
3ex8
UniProt (similar protein)
P17618
Target protein
KP13_02046

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 354.21 Da
LogP (Crippen) -3.46
H-bond donors 8
H-bond acceptors 9
TPSA 231.55 Ų
Rotatable bonds 7
Aromatic rings 1 / 1
Heavy atoms 23
Fraction sp³ C 0.44
Formula C₉H₁₅N₄O₉P

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 231.5
  • −1 ≤ LogP ≤ 5 -3.46
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 354.2
  • LogP ≤ 5 -3.46
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 231.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@H]([C@H]([C@@H](\C=N\C1=C(C(=O)NC(=O)N1)N)O)O)O)OP(=O)(O)O
InChI 
InChI=1S/C9H15N4O9P/c10-5-7(12-9(18)13-8(5)17)11-1-3(14)6(16)4(15)2-22-23(19,20)21/h1,3-4,6,14-16H,2,10H2,(H2,19,20,21)(H2,12,13,17,18)/b11-1+/t3-,4-,6+/m1/s1
InChIKey 
XKTZRTIKRCUGRX-QNGFKNCYSA-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
PF01872

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_02046.

PDB 6

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)