Ligand profile

6WB

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

Bound to: VK055_2316 — gpt

Via homolog PDB 5knt UniProt P0A9M2 Formula C₁₂H₂₀N₅O₆P
Mol. weight 361.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6WB
PDB
5knt
UniProt (similar protein)
P0A9M2
Target protein
VK055_2316

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 361.30 Da
LogP (Crippen) -2.05
H-bond donors 5
H-bond acceptors 8
TPSA 164.80 Ų
Rotatable bonds 9
Aromatic rings 2 / 2
Heavy atoms 24
Fraction sp³ C 0.58
Formula C₁₂H₂₀N₅O₆P

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 164.8
  • −1 ≤ LogP ≤ 5 -2.05
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 361.3
  • LogP ≤ 5 -2.05
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 164.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(n1CCN(CCP(=O)(O)O)C[C@@H](CO)O)N=CNC2=O
InChI 
InChI=1S/C12H20N5O6P/c18-6-9(19)5-16(3-4-24(21,22)23)1-2-17-8-15-10-11(17)13-7-14-12(10)20/h7-9,18-19H,1-6H2,(H,13,14,20)(H2,21,22,23)/t9-/m0/s1
InChIKey 
XBILBXZMSMIUBY-VIFPVBQESA-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)