Ligand profile

RFV

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

Bound to: KP13_31791 — RNA polymerase sigma factor RpoD

Via homolog PDB 4oir UniProt Q5SKW1 Formula C₃₇H₄₉NO₁₂
Mol. weight 699.79 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
RFV
PDB
4oir
UniProt (similar protein)
Q5SKW1
Target protein
KP13_31791

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 699.79 Da
LogP (Crippen) 4.60
H-bond donors 7
H-bond acceptors 12
TPSA 204.47 Ų
Rotatable bonds 2
Aromatic rings 2 / 5
Heavy atoms 50
Fraction sp³ C 0.51
Formula C₃₇H₄₉NO₁₂

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 204.5
  • −1 ≤ LogP ≤ 5 4.60
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 699.8
  • LogP ≤ 5 4.60
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 204.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c2c3c(cc(c2O)NC(=O)C(=C/C=C/[C@@H]([C@@H]([C@H]([C@H]([C@H]([C@@H]([C@@H]([C@H](/C=C/O[C@@]4([C@@H](c3c1O4)O)C)OC)C)OC(=O)C)C)O)C)O)C)C)O)O
InChI 
InChI=1S/C37H49NO12/c1-16-11-10-12-17(2)36(46)38-23-15-24(40)26-27(32(23)44)31(43)21(6)34-28(26)35(45)37(8,50-34)48-14-13-25(47-9)18(3)33(49-22(7)39)20(5)30(42)19(4)29(16)41/h10-16,18-20,25,29-30,33,35,40-45H,1-9H3,(H,38,46)/b11-10+,14-13+,17-12?/t16-,18+,19+,20+,25-,29-,30+,33+,35+,37-/m0/s1
InChIKey 
OUOULRWGQDSKTQ-WHWQEOOISA-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
PF04539' '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)