Binder profile

1RM

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

Bound to: PA1455 — flagellar biosynthesis sigma factor FliA

Via homolog PDB 4kn7 UniProt P00579 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
PA1455

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.

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 search.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF04539' 'PF04565

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other binders for this protein

Quick navigation to other ligands bound to PA1455.

PDB 11

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)