Ligand profile

1RM

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

Bound to: KP13_31791 — RNA polymerase sigma factor RpoD

Via homolog PDB 4kn7 UniProt P00579 Formula C₅₆H₇₀N₆O₁₃
Mol. weight 1035.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1RM
PDB
4kn7
UniProt (similar protein)
P00579
Target protein
KP13_31791

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 1035.20 Da
LogP (Crippen) 6.62
H-bond donors 4
H-bond acceptors 18
TPSA 237.48 Ų
Rotatable bonds 11
Aromatic rings 3 / 8
Heavy atoms 75
Fraction sp³ C 0.50
Formula C₅₆H₇₀N₆O₁₃

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 237.5
  • −1 ≤ LogP ≤ 5 6.62
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 1035.2
  • LogP ≤ 5 6.62
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 18
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 237.5
PAINS Clean

No PAINS structural alerts detected.

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=CC=C(C(=O)NC(=C5C3=Nc6c(cccc6OCCCCN7CCN(CC7)CCn8ccnc8)O5)C2=O)C)C)O)C)O)C)OC(=O)C)C)OC)C)O
InChI 
InChI=1S/C56H70N6O13/c1-31-14-12-15-32(2)55(69)59-46-50(67)42-41(45-53(46)74-40-17-13-16-39(44(40)58-45)71-28-11-10-20-60-22-24-61(25-23-60)26-27-62-21-19-57-30-62)43-52(36(6)49(42)66)75-56(8,54(43)68)72-29-18-38(70-9)33(3)51(73-37(7)63)35(5)48(65)34(4)47(31)64/h12-19,21,29-31,33-35,38,47-48,51,64-66H,10-11,20,22-28H2,1-9H3,(H,59,69)/b14-12?,29-18+,32-15?/t31-,33+,34+,35+,38-,47-,48+,51+,56-/m0/s1
InChIKey 
BWDTVIVNIJMQGS-KIJHMXGLSA-N

Provenance

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

Method
LigQ sequence
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)