Ligand profile

5QF

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

Bound to: KP13_03630 — Acriflavine resistance protein B

Via homolog PDB 5ng5 UniProt P31224 Formula 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
KP13_03630

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.

  • TPSA ≤ 90 Ų 80.1
  • −1 ≤ LogP ≤ 5 3.92
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 Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF00873

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to KP13_03630.

PDB 33

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)