Ligand profile

6W9

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

Bound to: VK055_2316 — gpt

Via homolog PDB 5knv UniProt P0A9M2 Formula C₁₃H₂₃N₅O₇P₂
Mol. weight 423.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6W9
PDB
5knv
UniProt (similar protein)
P0A9M2
Target protein
VK055_2316

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 423.30 Da
LogP (Crippen) -0.44
H-bond donors 5
H-bond acceptors 7
TPSA 181.87 Ų
Rotatable bonds 11
Aromatic rings 2 / 2
Heavy atoms 27
Fraction sp³ C 0.62
Formula C₁₃H₂₃N₅O₇P₂

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 181.9
  • −1 ≤ LogP ≤ 5 -0.44
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 423.3
  • LogP ≤ 5 -0.44
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 181.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(n1CCN(CCCCP(=O)(O)O)CCP(=O)(O)O)N=CNC2=O
InChI 
InChI=1S/C13H23N5O7P2/c19-13-11-12(14-9-15-13)18(10-16-11)5-4-17(6-8-27(23,24)25)3-1-2-7-26(20,21)22/h9-10H,1-8H2,(H,14,15,19)(H2,20,21,22)(H2,23,24,25)
InChIKey 
UBBYDRJNNDXCEB-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)