Ligand profile

0NP

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

Bound to: VK055_2593 — thymidine phosphorylase

Via homolog PDB 4ead UniProt P07650 Formula C₉H₁₁FN₅O₄⁺
Mol. weight 272.22 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
0NP
PDB
4ead
UniProt (similar protein)
P07650
Target protein
VK055_2593

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 272.22 Da
LogP (Crippen) -1.32
H-bond donors 3
H-bond acceptors 7
TPSA 134.63 Ų
Rotatable bonds 3
Aromatic rings 1 / 2
Heavy atoms 19
Fraction sp³ C 0.56
Formula C₉H₁₁FN₅O₄⁺

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 134.6
  • −1 ≤ LogP ≤ 5 -1.32
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 272.2
  • LogP ≤ 5 -1.32
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 134.6
PAINS Alert

Matches PAINS filter: azo_A(324). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)N=[N+]=N)F
InChI 
InChI=1S/C9H10FN5O4/c10-6-7(13-14-11)4(3-16)19-8(6)15-2-1-5(17)12-9(15)18/h1-2,4,6-8,11,16H,3H2/p+1/t4-,6-,7-,8-/m1/s1
InChIKey 
YRIDFNZYEULFDH-XVFCMESISA-O

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF00591

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_2593.

PDB 6

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

Ligand PDB entry

ChEMBL 14

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)