Ligand profile

P0C

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

Bound to: KP13_03756 — Nucleoside permease nupC

Via homolog PDB 4pd8 UniProt Q9KPL5 Formula C₁₂H₁₅N₃O₅
Mol. weight 281.27 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
P0C
PDB
4pd8
UniProt (similar protein)
Q9KPL5
Target protein
KP13_03756

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 281.27 Da
LogP (Crippen) -1.36
H-bond donors 4
H-bond acceptors 7
TPSA 120.60 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 20
Fraction sp³ C 0.50
Formula C₁₂H₁₅N₃O₅

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 120.6
  • −1 ≤ LogP ≤ 5 -1.36
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 281.3
  • LogP ≤ 5 -1.36
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 120.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1=CC2=CN(C(=O)N=C2N1)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O
InChI 
InChI=1S/C12H15N3O5/c1-5-2-6-3-15(12(19)14-10(6)13-5)11-9(18)8(17)7(4-16)20-11/h2-3,7-9,11,16-18H,4H2,1H3,(H,13,14,19)/t7-,8-,9-,11-/m1/s1
InChIKey 
GCNYJWODKQPZDE-TURQNECASA-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)