Binder profile

1RL

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

Bound to: PA1455 — flagellar biosynthesis sigma factor FliA

Via homolog PDB 4kn4 UniProt P00579 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
PA1455

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.

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 TPW 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 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)