Binder profile

UM3

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

Bound to: PA3866 — pyocin protein

Via homolog PDB 2djh UniProt P18000 C9H13N2O8P
Mol. weight 308.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
UM3
PDB
2djh
UniProt (similar protein)
P18000
Target protein
PA3866

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 308.18 Da
LogP (Crippen) -1.71
H-bond donors 4
H-bond acceptors 7
TPSA 151.08 Ų
Rotatable bonds 4
Aromatic rings 1 / 2
Heavy atoms 20
Fraction sp³ C 0.56
Formula C9H13N2O8P

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 308.2
  • LogP ≤ 5 -1.71
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 151.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO)OP(=O)(O)O
InChI 
InChI=1S/C9H13N2O8P/c12-4-6-5(19-20(15,16)17)3-8(18-6)11-2-1-7(13)10-9(11)14/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
InChIKey 
LXKGKXYIAAKOCT-SHYZEUOFSA-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
PF12106

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 1

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)