Ligand profile

C9H

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

Bound to: KP13_03868 — 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase

Via homolog PDB 4b0c UniProt O33877 Formula C₇H₁₃N₃S
Mol. weight 171.27 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
C9H
PDB
4b0c
UniProt (similar protein)
O33877
Target protein
KP13_03868

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 171.27 Da
LogP (Crippen) 2.09
H-bond donors 1
H-bond acceptors 3
TPSA 41.57 Ų
Rotatable bonds 5
Aromatic rings 1 / 1
Heavy atoms 11
Fraction sp³ C 0.71
Formula C₇H₁₃N₃S

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 41.6
  • −1 ≤ LogP ≤ 5 2.09
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 171.3
  • LogP ≤ 5 2.09
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 41.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCSc1[nH]ncn1
InChI 
InChI=1S/C7H13N3S/c1-2-3-4-5-11-7-8-6-9-10-7/h6H,2-5H2,1H3,(H,8,9,10)
InChIKey 
YDSWCAZMHZEBFW-UHFFFAOYSA-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
PF07977

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_03868.

PDB 12

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)