Binder profile

ZINC3873855

Virtual-screening candidate from ZINC.

Bound to: PA2400 — pyoverdine biosynthesis protein PvdJ

Via homolog UniProt Q70LM7 C11H17N5O9P2
Tanimoto 0.85
Mol. weight 425.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC3873855
UniProt (similar protein)
Q70LM7
Tanimoto
0.855
Target protein
PA2400

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 425.23 Da
LogP (Crippen) -1.64
H-bond donors 6
H-bond acceptors 11
TPSA 223.37 Ų
Rotatable bonds 6
Aromatic rings 2 / 3
Heavy atoms 27
Fraction sp³ C 0.55
Formula C11H17N5O9P2

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 2 violations
  • MW ≤ 500 Da 425.2
  • LogP ≤ 5 -1.64
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 223.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@](=O)(O)CP(=O)(O)O)[C@@H](O)[C@@H]1O
InChI 
InChI=1S/C11H17N5O9P2/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(25-11)1-24-27(22,23)4-26(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H2,12,13,14)(H2,19,20,21)/t5-,7+,8-,11+/m0/s1
InChIKey 
OLCWZBFDIYXLAA-IZCITBFLSA-N

Provenance

Annotation context from LigQ_2 search.

Method
LigQ nearest_k
Query
APC
Homolog
Q70LM7

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 14

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 49

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)