Ligand profile

CHEMBL1233528

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_05165 — Pyridoxamine kinase

Via homolog UniProt O00764 Formula C₃₄H₅₀N₈O₃
pchembl 6.54 ~288.4 nM
Mol. weight 618.83 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL1233528
UniProt (similar protein)
O00764
pchembl
6.540 (~288.4 nM)
Target protein
KP13_05165

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 618.83 Da
LogP (Crippen) 4.27
H-bond donors 2
H-bond acceptors 9
TPSA 106.17 Ų
Rotatable bonds 10
Aromatic rings 2 / 6
Heavy atoms 45
Fraction sp³ C 0.65
Formula C₃₄H₅₀N₈O₃

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 106.2
  • −1 ≤ LogP ≤ 5 4.27
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 618.8
  • LogP ≤ 5 4.27
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 9
Veber's rules Pass
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 106.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC[C@@H]1C(=O)N(C)c2cnc(Nc3ccc(C(=O)N[C@H]4CC[C@H](N5CCN(CC6CC6)CC5)CC4)cc3OC)nc2N1C(C)C
InChI 
InChI=1S/C34H50N8O3/c1-6-28-33(44)39(4)29-20-35-34(38-31(29)42(28)22(2)3)37-27-14-9-24(19-30(27)45-5)32(43)36-25-10-12-26(13-11-25)41-17-15-40(16-18-41)21-23-7-8-23/h9,14,19-20,22-23,25-26,28H,6-8,10-13,15-18,21H2,1-5H3,(H,36,43)(H,35,37,38)/t25-,26-,28-/m1/s1
InChIKey 
SXNJFOWDRLKDSF-STROYTFGSA-N

Provenance

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

Method
LigQ nearest_k
Source
ChEMBL
Activity
Active
Binding sites
PF08543

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_05165.

PDB 13

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

Ligand PDB entry

ChEMBL 4

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)