Ligand profile

1RL

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

Bound to: KP13_31791 — RNA polymerase sigma factor RpoD

Via homolog PDB 4kn4 UniProt P00579 Formula C₄₉H₆₁N₃O₁₃
Mol. weight 900.04 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1RL
PDB
4kn4
UniProt (similar protein)
P00579
Target protein
KP13_31791

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 900.04 Da
LogP (Crippen) 6.67
H-bond donors 4
H-bond acceptors 15
TPSA 216.42 Ų
Rotatable bonds 8
Aromatic rings 2 / 6
Heavy atoms 65
Fraction sp³ C 0.49
Formula C₄₉H₆₁N₃O₁₃

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 216.4
  • −1 ≤ LogP ≤ 5 6.67
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 900.0
  • LogP ≤ 5 6.67
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 15
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 216.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCN(CC)CCOc1cccc2c1N=C3c4c5c(c(c6c4C(=O)[C@](O6)(O/C=C/C([C@H]([C@H]([C@@H]([C@@H]([C@@H]([C@H]([C@H](C=CC=C(C(=O)NC(=C3O2)C5=O)C)C)O)C)O)C)OC(=O)C)C)OC)C)C)O
InChI 
InChI=1S/C49H61N3O13/c1-12-52(13-2)21-23-61-32-18-15-19-33-37(32)50-38-34-35-42(56)29(8)45-36(34)47(58)49(10,65-45)62-22-20-31(60-11)26(5)44(63-30(9)53)28(7)41(55)27(6)40(54)24(3)16-14-17-25(4)48(59)51-39(43(35)57)46(38)64-33/h14-20,22,24,26-28,31,40-41,44,54-56H,12-13,21,23H2,1-11H3,(H,51,59)/b16-14?,22-20+,25-17?/t24-,26+,27+,28+,31?,40-,41+,44+,49-/m0/s1
InChIKey 
NCYSEZCFZIFVEB-PVAZYGHZSA-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)