Ligand profile

KNH

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

Bound to: HT085_RS00370 — signal peptidase II

Via homolog PDB 6ryp UniProt Q6GHN9 Formula C₃₅H₆₁NO₈
Mol. weight 623.87 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
KNH
PDB
6ryp
UniProt (similar protein)
Q6GHN9
Target protein
HT085_RS00370

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 623.87 Da
LogP (Crippen) 5.20
H-bond donors 4
H-bond acceptors 8
TPSA 142.39 Ų
Rotatable bonds 5
Aromatic rings 0 / 1
Heavy atoms 44
Fraction sp³ C 0.80
Formula C₃₅H₆₁NO₈

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.

  • TPSA ≤ 90 Ų 142.4
  • −1 ≤ LogP ≤ 5 5.20
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 623.9
  • LogP ≤ 5 5.20
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 142.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCC[C@H]1C(=O)NC[C@H](C[C@@H]([C@@H](CC/C(=C/C=C\[C@@H](CCCC(=O)CCCC[C@H](C[C@@H](C(=O)O1)C)C)CC)/COC)O)O)O
InChI 
InChI=1S/C35H61NO8/c1-6-12-33-34(41)36-23-30(38)22-32(40)31(39)20-19-28(24-43-5)16-10-14-27(7-2)15-11-18-29(37)17-9-8-13-25(3)21-26(4)35(42)44-33/h10,14,16,25-27,30-33,38-40H,6-9,11-13,15,17-24H2,1-5H3,(H,36,41)/b14-10-,28-16-/t25-,26+,27+,30+,31-,32+,33+/m1/s1
InChIKey 
VQWNGCSUNKJFLW-ROEOKSPKSA-N

Provenance

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

Method
LigQ nearest_k
Source
PDB
Binding sites
PF01252

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to HT085_RS00370.

PDB 2

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)