Ligand profile

GEO

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

Bound to: KP13_03756 — Nucleoside permease nupC

Via homolog PDB 4pd5 UniProt Q9KPL5 Formula C₉H₁₁F₂N₃O₄
Mol. weight 263.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GEO
PDB
4pd5
UniProt (similar protein)
Q9KPL5
Target protein
KP13_03756

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 263.20 Da
LogP (Crippen) -1.29
H-bond donors 3
H-bond acceptors 7
TPSA 110.60 Ų
Rotatable bonds 2
Aromatic rings 1 / 2
Heavy atoms 18
Fraction sp³ C 0.56
Formula C₉H₁₁F₂N₃O₄

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 110.6
  • −1 ≤ LogP ≤ 5 -1.29
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 263.2
  • LogP ≤ 5 -1.29
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 110.6
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)CO)O)(F)F
InChI 
InChI=1S/C9H11F2N3O4/c10-9(11)6(16)4(3-15)18-7(9)14-2-1-5(12)13-8(14)17/h1-2,4,6-7,15-16H,3H2,(H2,12,13,17)/t4-,6-,7-/m1/s1
InChIKey 
SDUQYLNIPVEERB-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
PF07662' 'PF07670

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_03756.

PDB 9

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)