Ligand profile

AFX

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

Bound to: KP13_04751 — Adenosylhomocysteinase

Via homolog PDB 3nj4 UniProt P23526 Formula C₁₁H₁₀FN₅O₃
Mol. weight 279.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
AFX
PDB
3nj4
UniProt (similar protein)
P23526
Target protein
KP13_04751

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 279.23 Da
LogP (Crippen) -0.89
H-bond donors 3
H-bond acceptors 8
TPSA 127.15 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 20
Fraction sp³ C 0.27
Formula C₁₁H₁₀FN₅O₃

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 127.2
  • −1 ≤ LogP ≤ 5 -0.89
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 279.2
  • LogP ≤ 5 -0.89
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 127.2
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(=O)C(=C3F)CO)O)N
InChI 
InChI=1S/C11H10FN5O3/c12-5-4(1-18)8(19)9(20)7(5)17-3-16-6-10(13)14-2-15-11(6)17/h2-3,7,9,18,20H,1H2,(H2,13,14,15)/t7-,9+/m1/s1
InChIKey 
DMGPQGOOCCLGOU-APPZFPTMSA-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
PF00670' 'PF05221

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_04751.

PDB 6

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

Ligand PDB entry

ChEMBL 100

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)