Ligand profile

3L7

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

Bound to: VK055_2316 — gpt

Via homolog PDB 5kns UniProt P0A9M2 Formula C₁₃H₂₁N₅O₈P₂
Mol. weight 437.29 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3L7
PDB
5kns
UniProt (similar protein)
P0A9M2
Target protein
VK055_2316

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 437.29 Da
LogP (Crippen) -0.74
H-bond donors 5
H-bond acceptors 8
TPSA 191.10 Ų
Rotatable bonds 11
Aromatic rings 2 / 2
Heavy atoms 28
Fraction sp³ C 0.46
Formula C₁₃H₂₁N₅O₈P₂

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 191.1
  • −1 ≤ LogP ≤ 5 -0.74
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 437.3
  • LogP ≤ 5 -0.74
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 191.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(n1CCN(CCO/C=C/P(=O)(O)O)CCP(=O)(O)O)N=CNC2=O
InChI 
InChI=1S/C13H21N5O8P2/c19-13-11-12(14-9-15-13)18(10-16-11)2-1-17(4-7-27(20,21)22)3-5-26-6-8-28(23,24)25/h6,8-10H,1-5,7H2,(H,14,15,19)(H2,20,21,22)(H2,23,24,25)/b8-6+
InChIKey 
SGNFOZIWXPTVIN-SOFGYWHQSA-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)