Ligand profile

CHEMBL3944678

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_05165 — Pyridoxamine kinase

Via homolog UniProt O00764 Formula C₄₃H₅₄N₈O₉S₃
Mol. weight 923.15 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL3944678
UniProt (similar protein)
O00764
Target protein
KP13_05165

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 923.15 Da
LogP (Crippen) 3.73
H-bond donors 3
H-bond acceptors 15
TPSA 195.55 Ų
Rotatable bonds 22
Aromatic rings 4 / 8
Heavy atoms 63
Fraction sp³ C 0.51
Formula C₄₃H₅₄N₈O₉S₃

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 195.6
  • −1 ≤ LogP ≤ 5 3.73
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 923.2
  • LogP ≤ 5 3.73
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 15
Veber's rules Fail
  • Rotatable bonds ≤ 10 22
  • TPSA ≤ 140 Ų 195.6
PAINS Alert

Matches PAINS filter: anil_di_alk_C(246). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@@H]21)NCCOCCOCCOCCn1cc(COc2ccc(N3CCN(C(=O)c4cc5c(s4)-c4ccccc4S(=O)(=O)C5)CC3)cc2)nn1
InChI 
InChI=1S/C43H54N8O9S3/c52-39(8-4-2-6-36-40-35(28-61-36)45-43(54)46-40)44-13-19-57-21-23-59-24-22-58-20-18-51-26-31(47-48-51)27-60-33-11-9-32(10-12-33)49-14-16-50(17-15-49)42(53)37-25-30-29-63(55,56)38-7-3-1-5-34(38)41(30)62-37/h1,3,5,7,9-12,25-26,35-36,40H,2,4,6,8,13-24,27-29H2,(H,44,52)(H2,45,46,54)/t35-,36-,40-/m0/s1
InChIKey 
UHTZSHFDYVGELL-VXMGAWDISA-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)