Ligand profile

CHEMBL3989697

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_00855 — 3-mercaptopyruvate sulfurtransferase

Via homolog UniProt Q16762 Formula C₁₇H₂₄N₄NaO₁₁P
pchembl 6.42 ~380.2 nM
Mol. weight 514.36 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL3989697
UniProt (similar protein)
Q16762
pchembl
6.420 (~380.2 nM)
Target protein
KP13_00855

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 514.36 Da
LogP (Crippen) -6.88
H-bond donors 5
H-bond acceptors 11
TPSA 273.92 Ų
Rotatable bonds 7
Aromatic rings 1 / 3
Heavy atoms 34
Fraction sp³ C 0.41
Formula C₁₇H₂₄N₄NaO₁₁P

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 273.9
  • −1 ≤ LogP ≤ 5 -6.88
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 514.4
  • LogP ≤ 5 -6.88
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 273.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)[C@H](O)COP(=O)([O-])O)c2cc1C.O.O.[Na+]
InChI 
InChI=1S/C17H21N4O9P.Na.2H2O/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29;;;/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29);;2*1H2/q;+1;;/p-1/t11-,12+,14-;;;/m0.../s1
InChIKey 
LQVGUKOCMOKKJU-QPVGXXQTSA-M

Provenance

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

Method
LigQ nearest_k
Source
ChEMBL
Binding sites
PF00581

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_00855.

PDB 5

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

Ligand PDB entry

ChEMBL 7

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)