Binder profile

ZINC8613543

Virtual-screening candidate from ZINC.

Bound to: PA3866 — pyocin protein

Via homolog UniProt P18000 C10H13N5O4
Tanimoto 0.73
Mol. weight 267.24 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC8613543
UniProt (similar protein)
P18000
Tanimoto
0.732
Target protein
PA3866

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 267.24 Da
LogP (Crippen) -1.66
H-bond donors 4
H-bond acceptors 8
TPSA 139.28 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 19
Fraction sp³ C 0.50
Formula C10H13N5O4

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 0 violations
  • MW ≤ 500 Da 267.2
  • LogP ≤ 5 -1.66
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 139.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1nc2c(ncn2[C@@H]2C[C@@H](O)[C@@H](CO)O2)c(=O)[nH]1
InChI 
InChI=1S/C10H13N5O4/c11-10-13-8-7(9(18)14-10)12-3-15(8)6-1-4(17)5(2-16)19-6/h3-6,16-17H,1-2H2,(H3,11,13,14,18)/t4-,5-,6+/m1/s1
InChIKey 
YKBGVTZYEHREMT-PBXRRBTRSA-N

Provenance

Annotation context from LigQ_2, the internal TPW step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
3PD
Homolog
P18000

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA3866.

PDB 2

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)