Ligand profile

RBV

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

Bound to: KP13_03756 — Nucleoside permease nupC

Via homolog PDB 4pb1 UniProt Q9KPL5 Formula C₈H₁₂N₄O₅
Mol. weight 244.21 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
RBV
PDB
4pb1
UniProt (similar protein)
Q9KPL5
Target protein
KP13_03756

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 244.21 Da
LogP (Crippen) -3.01
H-bond donors 4
H-bond acceptors 8
TPSA 143.72 Ų
Rotatable bonds 3
Aromatic rings 1 / 2
Heavy atoms 17
Fraction sp³ C 0.62
Formula C₈H₁₂N₄O₅

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 143.7
  • −1 ≤ LogP ≤ 5 -3.01
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 244.2
  • LogP ≤ 5 -3.01
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 143.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(nn1[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O)C(=O)N
InChI 
InChI=1S/C8H12N4O5/c9-6(16)7-10-2-12(11-7)8-5(15)4(14)3(1-13)17-8/h2-5,8,13-15H,1H2,(H2,9,16)/t3-,4-,5-,8-/m1/s1
InChIKey 
IWUCXVSUMQZMFG-AFCXAGJDSA-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)