Binder profile

JSJ

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

Bound to: PA0413 — chemotactic signal transduction system protein

Via homolog PDB 6mi6 UniProt Q56310 C19H30N6O10P2S2
Mol. weight 628.56 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JSJ
PDB
6mi6
UniProt (similar protein)
Q56310
Target protein
PA0413

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 628.56 Da
LogP (Crippen) 1.83
H-bond donors 6
H-bond acceptors 16
TPSA 235.84 Ų
Rotatable bonds 10
Aromatic rings 2 / 4
Heavy atoms 39
Fraction sp³ C 0.63
Formula C19H30N6O10P2S2

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 628.6
  • LogP ≤ 5 1.83
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 16
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 235.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1(C=C(C(N1O)(C)C)CSSP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)C
InChI 
InChI=1S/C19H30N6O10P2S2/c1-18(2)5-10(19(3,4)25(18)28)7-38-39-37(31,32)35-36(29,30)33-6-11-13(26)14(27)17(34-11)24-9-23-12-15(20)21-8-22-16(12)24/h5,8-9,11,13-14,17,26-28H,6-7H2,1-4H3,(H,29,30)(H,31,32)(H2,20,21,22)/t11-,13-,14-,17-/m1/s1
InChIKey 
FXTBVPRAZDKBSQ-LSCFUAHRSA-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
PF02518

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA0413.

PDB 4

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)