Ligand profile

3L5

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

Bound to: VK055_2316 — gpt

Via homolog PDB 5knr UniProt P0A9M2 Formula C₁₃H₂₄N₆O₈P₂
Mol. weight 454.32 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3L5
PDB
5knr
UniProt (similar protein)
P0A9M2
Target protein
VK055_2316

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 454.32 Da
LogP (Crippen) -1.62
H-bond donors 6
H-bond acceptors 9
TPSA 217.12 Ų
Rotatable bonds 12
Aromatic rings 2 / 2
Heavy atoms 29
Fraction sp³ C 0.62
Formula C₁₃H₂₄N₆O₈P₂

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 217.1
  • −1 ≤ LogP ≤ 5 -1.62
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 454.3
  • LogP ≤ 5 -1.62
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 217.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(n1CCN(CCOCCP(=O)(O)O)CCP(=O)(O)O)NC(=NC2=O)N
InChI 
InChI=1S/C13H24N6O8P2/c14-13-16-11-10(12(20)17-13)15-9-19(11)2-1-18(4-7-28(21,22)23)3-5-27-6-8-29(24,25)26/h9H,1-8H2,(H2,21,22,23)(H2,24,25,26)(H3,14,16,17,20)
InChIKey 
ONMAFLJUDYCSLA-UHFFFAOYSA-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
PF00156

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_2316.

PDB 14

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)