Ligand profile

GTF

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

Bound to: KP13_03062 — putative metal-dependent phosphohydrolase

Via homolog PDB 6dw5 UniProt Q9Y3Z3 Formula C₉H₁₄F₂N₃O₁₃P₃
Mol. weight 503.14 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GTF
PDB
6dw5
UniProt (similar protein)
Q9Y3Z3
Target protein
KP13_03062

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 503.14 Da
LogP (Crippen) -0.94
H-bond donors 6
H-bond acceptors 12
TPSA 250.19 Ų
Rotatable bonds 8
Aromatic rings 1 / 2
Heavy atoms 30
Fraction sp³ C 0.56
Formula C₉H₁₄F₂N₃O₁₃P₃

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 250.2
  • −1 ≤ LogP ≤ 5 -0.94
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 503.1
  • LogP ≤ 5 -0.94
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 250.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1=CN(C(=O)N=C1N)[C@H]2C([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)(F)F
InChI 
InChI=1S/C9H14F2N3O13P3/c10-9(11)6(15)4(25-7(9)14-2-1-5(12)13-8(14)16)3-24-29(20,21)27-30(22,23)26-28(17,18)19/h1-2,4,6-7,15H,3H2,(H,20,21)(H,22,23)(H2,12,13,16)(H2,17,18,19)/t4-,6-,7-/m1/s1
InChIKey 
YMOXEIOKAJSRQX-QPPQHZFASA-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)