Ligand profile

ZINC95628816

Virtual-screening candidate from ZINC.

Bound to: KP13_03548 — Pyridoxine kinase

Via homolog UniProt O00764 Formula C₂₀H₂₅N₅O₄
Tanimoto 0.71
Mol. weight 399.45 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC95628816
UniProt (similar protein)
O00764
Tanimoto
0.709
Target protein
KP13_03548

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 399.45 Da
LogP (Crippen) 2.90
H-bond donors 2
H-bond acceptors 7
TPSA 107.89 Ų
Rotatable bonds 6
Aromatic rings 2 / 3
Heavy atoms 29
Fraction sp³ C 0.40
Formula C₂₀H₂₅N₅O₄

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 107.9
  • −1 ≤ LogP ≤ 5 2.90
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 399.5
  • LogP ≤ 5 2.90
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 107.9
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)O)cc3OC)nc2N1C(C)C
InChI 
InChI=1S/C20H25N5O4/c1-6-14-18(26)24(4)15-10-21-20(23-17(15)25(14)11(2)3)22-13-8-7-12(19(27)28)9-16(13)29-5/h7-11,14H,6H2,1-5H3,(H,27,28)(H,21,22,23)/t14-/m1/s1
InChIKey 
QNLSHJVWZNHSED-CQSZACIVSA-N

Provenance

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

Method
LigQ nearest_k
Query
CHEMBL1233528
Homolog
O00764

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_03548.

PDB 8

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 49

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)