Ligand profile

P3F

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

Bound to: KP13_02775 — Cystathionine beta-lyase metC

Via homolog PDB 2fq6 UniProt P06721 Formula C₁₈H₁₈F₃N₄O₇P
Mol. weight 490.33 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
P3F
PDB
2fq6
UniProt (similar protein)
P06721
Target protein
KP13_02775

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 490.33 Da
LogP (Crippen) 1.60
H-bond donors 5
H-bond acceptors 7
TPSA 170.44 Ų
Rotatable bonds 8
Aromatic rings 2 / 2
Heavy atoms 33
Fraction sp³ C 0.22
Formula C₁₈H₁₈F₃N₄O₇P

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 170.4
  • −1 ≤ LogP ≤ 5 1.60
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 490.3
  • LogP ≤ 5 1.60
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 170.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c(cn1)COP(=O)(O)O)\C=N\NC(=O)CNC(=O)c2ccccc2C(F)(F)F)O
InChI 
InChI=1S/C18H18F3N4O7P/c1-10-16(27)13(11(6-22-10)9-32-33(29,30)31)7-24-25-15(26)8-23-17(28)12-4-2-3-5-14(12)18(19,20)21/h2-7,27H,8-9H2,1H3,(H,23,28)(H,25,26)(H2,29,30,31)/b24-7+
InChIKey 
MCLYFEQPXXDFPI-HCBMXOAHSA-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
PF01053

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_02775.

PDB 16

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

Ligand PDB entry

ChEMBL 4

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)