Ligand profile

CHEMBL1365553

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_1238 — exodeoxyribonuclease III

Via homolog UniProt P27695 Formula C₂₉H₁₇ClN₇Na₃O₁₁S₃
pchembl 6.60 ~251.2 nM
Mol. weight 840.12 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL1365553
UniProt (similar protein)
P27695
pchembl
6.600 (~251.2 nM)
Target protein
VK055_1238

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 840.12 Da
LogP (Crippen) -6.16
H-bond donors 4
H-bond acceptors 18
TPSA 306.52 Ų
Rotatable bonds 9
Aromatic rings 5 / 6
Heavy atoms 54
Fraction sp³ C 0.00
Formula C₂₉H₁₇ClN₇Na₃O₁₁S₃

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 306.5
  • −1 ≤ LogP ≤ 5 -6.16
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 840.1
  • LogP ≤ 5 -6.16
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 18
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 306.5
PAINS Alert

Matches PAINS filter: quinone_A(370). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1c(S(=O)(=O)[O-])cc(Nc2ccc(Nc3nc(Cl)nc(Nc4ccc(S(=O)(=O)[O-])cc4)n3)c(S(=O)(=O)[O-])c2)c2c1C(=O)c1ccccc1C2=O.[Na+].[Na+].[Na+]
InChI 
InChI=1S/C29H20ClN7O11S3.3Na/c30-27-35-28(33-13-5-8-15(9-6-13)49(40,41)42)37-29(36-27)34-18-10-7-14(11-20(18)50(43,44)45)32-19-12-21(51(46,47)48)24(31)23-22(19)25(38)16-3-1-2-4-17(16)26(23)39;;;/h1-12,32H,31H2,(H,40,41,42)(H,43,44,45)(H,46,47,48)(H2,33,34,35,36,37);;;/q;3*+1/p-3
InChIKey 
WDPGNDHCHKUGLY-UHFFFAOYSA-K

Provenance

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

Method
LigQ nearest_k
Source
ChEMBL
Activity
Active
Binding sites
PF03372

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_1238.

PDB 1

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)