Ligand profile

6WA

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

Bound to: VK055_2316 — gpt

Via homolog PDB 5knu UniProt P0A9M2 Formula C₁₃H₂₂N₄O₇P₂
Mol. weight 408.29 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6WA
PDB
5knu
UniProt (similar protein)
P0A9M2
Target protein
VK055_2316

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 408.29 Da
LogP (Crippen) 0.19
H-bond donors 6
H-bond acceptors 5
TPSA 179.84 Ų
Rotatable bonds 10
Aromatic rings 2 / 2
Heavy atoms 26
Fraction sp³ C 0.54
Formula C₁₃H₂₂N₄O₇P₂

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 179.8
  • −1 ≤ LogP ≤ 5 0.19
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 408.3
  • LogP ≤ 5 0.19
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 5
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 179.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c(c2c([nH]1)C(=O)NC=N2)CN(CCCP(=O)(O)O)CCCP(=O)(O)O
InChI 
InChI=1S/C13H22N4O7P2/c18-13-12-11(15-9-16-13)10(7-14-12)8-17(3-1-5-25(19,20)21)4-2-6-26(22,23)24/h7,9,14H,1-6,8H2,(H,15,16,18)(H2,19,20,21)(H2,22,23,24)
InChIKey 
UJUSHVYEYJBIDB-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)