Ligand profile

SRN

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

Bound to: KP13_31791 — RNA polymerase sigma factor RpoD

Via homolog PDB 6vvx UniProt P9WGI1 Formula C₄₇H₆₆O₁₁
Mol. weight 807.03 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SRN
PDB
6vvx
UniProt (similar protein)
P9WGI1
Target protein
KP13_31791

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 807.03 Da
LogP (Crippen) 6.80
H-bond donors 4
H-bond acceptors 10
TPSA 161.21 Ų
Rotatable bonds 7
Aromatic rings 0 / 6
Heavy atoms 58
Fraction sp³ C 0.62
Formula C₄₇H₆₆O₁₁

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 161.2
  • −1 ≤ LogP ≤ 5 6.80
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 807.0
  • LogP ≤ 5 6.80
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 161.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H]1[C@H]2C\C=C\[C@H]3[C@@H]([C@H]4C[C@@H](O3)[C@H](O4)/C=C/C=C\C=C/C(=O)O[C@H]5C=C[C@H](C\C=C\CC\C=C\[C@@H]([C@@H]([C@H](O2)C[C@@H]1O)O)O)O[C@H]5/C(=C/[C@H](C)CCCCC(=O)O)/C)C
InChI 
InChI=1S/C47H66O11/c1-30(17-14-15-23-44(50)51)27-31(2)47-40-26-25-34(54-47)18-10-6-5-7-11-19-35(48)46(53)43-28-36(49)32(3)37(56-43)21-16-22-38-33(4)41-29-42(55-38)39(57-41)20-12-8-9-13-24-45(52)58-40/h6,8-13,16,19-20,22,24-27,30,32-43,46-49,53H,5,7,14-15,17-18,21,23,28-29H2,1-4H3,(H,50,51)/b9-8-,10-6+,19-11+,20-12+,22-16+,24-13-,31-27+/t30-,32-,33+,34+,35+,36+,37-,38+,39-,40+,41-,42-,43-,46+,47+/m1/s1
InChIKey 
OTABDKFPJQZJRD-QLGZCQHWSA-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 KP13_31791.

PDB 12

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

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)