Ligand profile

PN4

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

Bound to: KP13_03141 — Uridine kinase

Via homolog PDB 4f7w UniProt B5XYG3 Formula C₁₄H₂₈N₂O₄
Mol. weight 288.39 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PN4
PDB
4f7w
UniProt (similar protein)
B5XYG3
Target protein
KP13_03141

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 288.39 Da
LogP (Crippen) 0.18
H-bond donors 4
H-bond acceptors 4
TPSA 98.66 Ų
Rotatable bonds 10
Aromatic rings 0 / 0
Heavy atoms 20
Fraction sp³ C 0.86
Formula C₁₄H₂₈N₂O₄

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 98.7
  • −1 ≤ LogP ≤ 5 0.18
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 288.4
  • LogP ≤ 5 0.18
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 98.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO)O
InChI 
InChI=1S/C14H28N2O4/c1-4-5-6-8-15-11(18)7-9-16-13(20)12(19)14(2,3)10-17/h12,17,19H,4-10H2,1-3H3,(H,15,18)(H,16,20)/t12-/m0/s1
InChIKey 
HWNKKPMQPCHGBA-LBPRGKRZSA-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
PF00485

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_03141.

PDB 11

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

Ligand PDB entry

ChEMBL 2

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)