Ligand profile

HFD

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

Bound to: KP13_03062 — putative metal-dependent phosphohydrolase

Via homolog PDB 6dwk UniProt Q9Y3Z3 Formula C₁₀H₁₅FN₅O₁₃P₃
Mol. weight 525.17 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HFD
PDB
6dwk
UniProt (similar protein)
Q9Y3Z3
Target protein
KP13_03062

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 525.17 Da
LogP (Crippen) -1.49
H-bond donors 7
H-bond acceptors 14
TPSA 279.13 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 32
Fraction sp³ C 0.50
Formula C₁₀H₁₅FN₅O₁₃P₃

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 279.1
  • −1 ≤ LogP ≤ 5 -1.49
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 525.2
  • LogP ≤ 5 -1.49
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 279.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(nc(nc2n1[C@H]3[C@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)F)N
InChI 
InChI=1S/C10H15FN5O13P3/c11-10-14-7(12)4-8(15-10)16(2-13-4)9-6(18)5(17)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,17-18H,1H2,(H,22,23)(H,24,25)(H2,12,14,15)(H2,19,20,21)/t3-,5-,6+,9-/m1/s1
InChIKey 
PIOKUWLZUXUBCO-FJFJXFQQSA-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
PF01966

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_03062.

PDB 22

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

Ligand PDB entry

ChEMBL 1

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)