Binder profile

CO8

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

Bound to: PA2400 — pyoverdine biosynthesis protein PvdJ

Via homolog PDB 7c1r UniProt E5ATN9 C29H50N7O17P3S
Mol. weight 893.74 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CO8
PDB
7c1r
UniProt (similar protein)
E5ATN9
Target protein
PA2400

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 893.74 Da
LogP (Crippen) 1.03
H-bond donors 9
H-bond acceptors 19
TPSA 363.63 Ų
Rotatable bonds 25
Aromatic rings 2 / 3
Heavy atoms 57
Fraction sp³ C 0.72
Formula C29H50N7O17P3S

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 893.7
  • LogP ≤ 5 1.03
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 19
Veber's rules Fail
  • Rotatable bonds ≤ 10 25
  • TPSA ≤ 140 Ų 363.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
InChI 
InChI=1S/C29H50N7O17P3S/c1-4-5-6-7-8-9-20(38)57-13-12-31-19(37)10-11-32-27(41)24(40)29(2,3)15-50-56(47,48)53-55(45,46)49-14-18-23(52-54(42,43)44)22(39)28(51-18)36-17-35-21-25(30)33-16-34-26(21)36/h16-18,22-24,28,39-40H,4-15H2,1-3H3,(H,31,37)(H,32,41)(H,45,46)(H,47,48)(H2,30,33,34)(H2,42,43,44)/t18-,22-,23-,24+,28-/m1/s1
InChIKey 
KQMZYOXOBSXMII-CECATXLMSA-N

Provenance

Annotation context from LigQ_2 search.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00668

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)