Ligand profile

CHEMBL1909658

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_3110 — DNA-directed RNA polymerase, beta subunit

Via homolog UniProt P9WGY9 Formula C₄₃H₅₆N₄O₁₂
pchembl 7.89 ~12.9 nM
Mol. weight 820.94 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL1909658
UniProt (similar protein)
P9WGY9
pchembl
7.890 (~12.9 nM)
Target protein
VK055_3110

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 820.94 Da
LogP (Crippen) 3.23
H-bond donors 4
H-bond acceptors 15
TPSA 213.83 Ų
Rotatable bonds 4
Aromatic rings 1 / 6
Heavy atoms 59
Fraction sp³ C 0.53
Formula C₄₃H₅₆N₄O₁₂

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 213.8
  • −1 ≤ LogP ≤ 5 3.23
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 820.9
  • LogP ≤ 5 3.23
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 15
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 213.8
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 
CO[C@H]1/C=C/O[C@@]2(C)Oc3c(C)c(O)c4c(c3C2=O)C(=O)C(/C=N/N2CCN(C)CC2)=C(NC(=O)/C(C)=C\C=C\[C@H](C)[C@H](O)[C@@H](C)[C@@H](O)[C@@H](C)[C@H](OC(C)=O)[C@@H]1C)C4=O
InChI 
InChI=1S/C43H56N4O12/c1-21-12-11-13-22(2)42(55)45-33-28(20-44-47-17-15-46(9)16-18-47)37(52)30-31(38(33)53)36(51)26(6)40-32(30)41(54)43(8,59-40)57-19-14-29(56-10)23(3)39(58-27(7)48)25(5)35(50)24(4)34(21)49/h11-14,19-21,23-25,29,34-35,39,49-51H,15-18H2,1-10H3,(H,45,55)/b12-11+,19-14+,22-13-,44-20+/t21-,23+,24+,25+,29-,34-,35+,39+,43-/m0/s1
InChIKey 
IHHAOHNZEKYBLG-WLSIYKJHSA-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
Curation
pdb_similarity_tanimoto
Binding sites
PF00562' 'PF04563' 'PF04565

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_3110.

PDB 35

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

Ligand PDB entry

ChEMBL 7

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)