Ligand profile

D95

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

Bound to: KP13_05165 — Pyridoxamine kinase

Via homolog PDB 6yk1 UniProt Q8K183 Formula C₁₉H₂₈O₈
Mol. weight 384.43 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
D95
PDB
6yk1
UniProt (similar protein)
Q8K183
Target protein
KP13_05165

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 384.43 Da
LogP (Crippen) 2.60
H-bond donors 1
H-bond acceptors 7
TPSA 100.52 Ų
Rotatable bonds 4
Aromatic rings 0 / 5
Heavy atoms 27
Fraction sp³ C 0.89
Formula C₁₉H₂₈O₈

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 100.5
  • −1 ≤ LogP ≤ 5 2.60
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 384.4
  • LogP ≤ 5 2.60
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 100.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]1CC[C@H]2[C@H]([C@@H](O[C@H]3[C@@]24[C@H]1CC[C@](O3)(OO4)C)OC(=O)CCC(=O)O)C
InChI 
InChI=1S/C19H28O8/c1-10-4-5-13-11(2)16(23-15(22)7-6-14(20)21)24-17-19(13)12(10)8-9-18(3,25-17)26-27-19/h10-13,16-17H,4-9H2,1-3H3,(H,20,21)/t10-,11-,12+,13+,16-,17-,18-,19-/m1/s1
InChIKey 
FIHJKUPKCHIPAT-AHIGJZGOSA-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
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 12

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

Ligand PDB entry

ChEMBL 5

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)