Ligand profile

GB8

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_2560 — chaperone protein DnaK

Via homolog UniProt P11021 Formula C₂₀H₂₁N₇O₄
pchembl 6.64 ~229.1 nM
Mol. weight 423.43 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GB8
UniProt (similar protein)
P11021
pchembl
6.640 (~229.1 nM)
Target protein
VK055_2560

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 423.43 Da
LogP (Crippen) 0.18
H-bond donors 5
H-bond acceptors 11
TPSA 164.46 Ų
Rotatable bonds 5
Aromatic rings 4 / 5
Heavy atoms 31
Fraction sp³ C 0.30
Formula C₂₀H₂₁N₇O₄

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 164.5
  • −1 ≤ LogP ≤ 5 0.18
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 423.4
  • LogP ≤ 5 0.18
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 164.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc2cc(ccc2nc1)CNc3nc4c(ncnc4n3[C@H]5[C@@H]([C@@H]([C@H](O5)CO)O)O)N
InChI 
InChI=1S/C20H21N7O4/c21-17-14-18(25-9-24-17)27(19-16(30)15(29)13(8-28)31-19)20(26-14)23-7-10-3-4-12-11(6-10)2-1-5-22-12/h1-6,9,13,15-16,19,28-30H,7-8H2,(H,23,26)(H2,21,24,25)/t13-,15-,16-,19-/m1/s1
InChIKey 
ZPAVHMFARWZWPX-NVQRDWNXSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
ChEMBL
Binding sites
PF00012

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_2560.

PDB 20

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 99

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)