Ligand profile

RPT

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

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

Via homolog PDB 2a69 UniProt Q8RQE9 Formula C₄₇H₆₄N₄O₁₂
Mol. weight 877.04 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
RPT
PDB
2a69
UniProt (similar protein)
Q8RQE9
Target protein
VK055_3110

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 877.04 Da
LogP (Crippen) 5.65
H-bond donors 6
H-bond acceptors 15
TPSA 220.15 Ų
Rotatable bonds 5
Aromatic rings 2 / 7
Heavy atoms 63
Fraction sp³ C 0.57
Formula C₄₇H₆₄N₄O₁₂

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 220.1
  • −1 ≤ LogP ≤ 5 5.65
Lipinski's Rule of Five Fail 4 violations
  • MW ≤ 500 Da 877.0
  • LogP ≤ 5 5.65
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 15
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 220.1
PAINS Alert

Matches PAINS filter: hzone_phenol_A(479). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c2c3c4c1O[C@@](C4=O)(O\C=C\[C@@H]([C@H]([C@H]([C@@H]([C@@H]([C@@H]([C@H]([C@H](\C=C\C=C(/C(=O)Nc(c2O)c(c3O)\C=N\N5CCN(CC5)C6CCCC6)\C)C)O)C)O)C)OC(=O)C)C)OC)C)O
InChI 
InChI=1S/C47H64N4O12/c1-24-13-12-14-25(2)46(59)49-37-32(23-48-51-20-18-50(19-21-51)31-15-10-11-16-31)41(56)34-35(42(37)57)40(55)29(6)44-36(34)45(58)47(8,63-44)61-22-17-33(60-9)26(3)43(62-30(7)52)28(5)39(54)27(4)38(24)53/h12-14,17,22-24,26-28,31,33,38-39,43,53-57H,10-11,15-16,18-21H2,1-9H3,(H,49,59)/b13-12+,22-17+,25-14-,48-23+/t24-,26+,27+,28+,33-,38-,39+,43+,47-/m0/s1
InChIKey 
WDZCUPBHRAEYDL-GZAUEHORSA-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
PF00562' 'PF04539' '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 34

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

Ligand PDB entry

ChEMBL 8

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)