Ligand profile

XFA

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

Bound to: KP13_04751 — Adenosylhomocysteinase

Via homolog PDB 4yvf UniProt P23526 Formula C₂₈H₃₁Cl₂N₅O₃
Mol. weight 556.49 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
XFA
PDB
4yvf
UniProt (similar protein)
P23526
Target protein
KP13_04751

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 556.49 Da
LogP (Crippen) 4.32
H-bond donors 2
H-bond acceptors 6
TPSA 77.15 Ų
Rotatable bonds 11
Aromatic rings 3 / 4
Heavy atoms 38
Fraction sp³ C 0.29
Formula C₂₈H₃₁Cl₂N₅O₃

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 77.1
  • −1 ≤ LogP ≤ 5 4.32
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 556.5
  • LogP ≤ 5 4.32
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 77.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CNCCNC(=O)CN(CC(=O)N(C)N1Cc2ccccc2C1)c3cc(ccc3Oc4ccc(cc4)Cl)Cl
InChI 
InChI=1S/C28H31Cl2N5O3/c1-31-13-14-32-27(36)18-34(19-28(37)33(2)35-16-20-5-3-4-6-21(20)17-35)25-15-23(30)9-12-26(25)38-24-10-7-22(29)8-11-24/h3-12,15,31H,13-14,16-19H2,1-2H3,(H,32,36)
InChIKey 
AOQCCSFIEWPXMC-UHFFFAOYSA-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)