Ligand profile

ATF

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

Bound to: KP13_03421 — Glycerol kinase

Via homolog PDB 1bwf UniProt P0A6F3 Formula C₁₁H₁₆F₂N₅O₁₂P₃
Mol. weight 541.19 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ATF
PDB
1bwf
UniProt (similar protein)
P0A6F3
Target protein
KP13_03421

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 541.19 Da
LogP (Crippen) -0.93
H-bond donors 7
H-bond acceptors 13
TPSA 269.90 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 33
Fraction sp³ C 0.55
Formula C₁₁H₁₆F₂N₅O₁₂P₃

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 269.9
  • −1 ≤ LogP ≤ 5 -0.93
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 541.2
  • LogP ≤ 5 -0.93
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 269.9
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@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(C(F)(F)P(=O)(O)O)O)O)O)N
InChI 
InChI=1S/C11H16F2N5O12P3/c12-11(13,31(21,22)23)32(24,25)30-33(26,27)28-1-4-6(19)7(20)10(29-4)18-3-17-5-8(14)15-2-16-9(5)18/h2-4,6-7,10,19-20H,1H2,(H,24,25)(H,26,27)(H2,14,15,16)(H2,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKey 
ODWAWOIUPXBZKQ-KQYNXXCUSA-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
PF00370' 'PF02782

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_03421.

PDB 12

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)