Ligand profile

H9V

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

Bound to: KP13_05358 — Tryptophan synthase beta chain

Via homolog PDB 6uap UniProt P9WFX9 Formula C₁₇H₁₂ClF₃N₂
Mol. weight 336.74 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
H9V
PDB
6uap
UniProt (similar protein)
P9WFX9
Target protein
KP13_05358

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 336.74 Da
LogP (Crippen) 4.20
H-bond donors 1
H-bond acceptors 2
TPSA 35.82 Ų
Rotatable bonds 3
Aromatic rings 2 / 3
Heavy atoms 23
Fraction sp³ C 0.24
Formula C₁₇H₁₂ClF₃N₂

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 35.8
  • −1 ≤ LogP ≤ 5 4.20
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 336.7
  • LogP ≤ 5 4.20
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 35.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1c2c(cc(cc2F)Cl)F)C3C(NC3C#N)CF
InChI 
InChI=1S/C17H12ClF3N2/c18-11-5-12(20)16(13(21)6-11)9-1-3-10(4-2-9)17-14(7-19)23-15(17)8-22/h1-6,14-15,17,23H,7H2
InChIKey 
XHUZEPHBFHVYMY-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
PF00290' 'PF00291

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_05358.

PDB 40

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)