Binder profile

5QF

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

Bound to: PA3676 — resistance-nodulation-cell division (RND) efflux transporter

Via homolog PDB 5ng5 UniProt P31224 C28H38N4O4S
Mol. weight 526.70 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5QF
PDB
5ng5
UniProt (similar protein)
P31224
Target protein
PA3676

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 526.70 Da
LogP (Crippen) 3.92
H-bond donors 0
H-bond acceptors 9
TPSA 80.08 Ų
Rotatable bonds 10
Aromatic rings 2 / 4
Heavy atoms 37
Fraction sp³ C 0.57
Formula C28H38N4O4S

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 526.7
  • LogP ≤ 5 3.92
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 9
Veber's rules Pass
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 80.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1(Cc2c(c(nc(c2C#N)SCCc3ccc(c(c3)OC)OC)N4CCN(CC4)CCOC)CO1)C
InChI 
InChI=1S/C28H38N4O4S/c1-28(2)17-21-22(18-29)27(37-15-8-20-6-7-24(34-4)25(16-20)35-5)30-26(23(21)19-36-28)32-11-9-31(10-12-32)13-14-33-3/h6-7,16H,8-15,17,19H2,1-5H3
InChIKey 
PJMAUCHUUURBGI-UHFFFAOYSA-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
PF00873

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA3676.

PDB 32

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

Ligand PDB entry

ChEMBL 53

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)