Binder profile

5S4

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

Bound to: PA2400 — pyoverdine biosynthesis protein PvdJ

Via homolog PDB 5es8 UniProt Q70LM7 C16H33N4O8P
Mol. weight 440.43 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5S4
PDB
5es8
UniProt (similar protein)
Q70LM7
Target protein
PA2400

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 440.43 Da
LogP (Crippen) -1.80
H-bond donors 7
H-bond acceptors 7
TPSA 200.31 Ų
Rotatable bonds 13
Aromatic rings 0 / 0
Heavy atoms 29
Fraction sp³ C 0.81
Formula C16H33N4O8P

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 Pass 1 violation
  • MW ≤ 500 Da 440.4
  • LogP ≤ 5 -1.80
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 13
  • TPSA ≤ 140 Ų 200.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)[C@@H](C(=O)NCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)O)O)N
InChI 
InChI=1S/C16H33N4O8P/c1-10(2)12(17)14(23)20-8-7-18-11(21)5-6-19-15(24)13(22)16(3,4)9-28-29(25,26)27/h10,12-13,22H,5-9,17H2,1-4H3,(H,18,21)(H,19,24)(H,20,23)(H2,25,26,27)/t12-,13-/m0/s1
InChIKey 
MFHZIFARQCIIMR-STQMWFEESA-N

Provenance

Annotation context from LigQ_2 search.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00501' 'PF00550

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA2400.

PDB 13

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)