Ligand profile

HDF

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

Bound to: KP13_03293 — Deoxyribodipyrimidine photo-lyase

Via homolog PDB 1qnf UniProt P05327 Formula C₁₆H₁₇N₃O₇
Mol. weight 363.33 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HDF
PDB
1qnf
UniProt (similar protein)
P05327
Target protein
KP13_03293

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 363.33 Da
LogP (Crippen) -2.03
H-bond donors 6
H-bond acceptors 9
TPSA 168.90 Ų
Rotatable bonds 5
Aromatic rings 1 / 3
Heavy atoms 26
Fraction sp³ C 0.31
Formula C₁₆H₁₇N₃O₇

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 168.9
  • −1 ≤ LogP ≤ 5 -2.03
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 363.3
  • LogP ≤ 5 -2.03
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 168.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc2c(cc1O)N(C3=NC(=O)NC(=O)C3=C2)C[C@H]([C@@H]([C@H](CO)O)O)O
InChI 
InChI=1S/C16H17N3O7/c20-6-12(23)13(24)11(22)5-19-10-4-8(21)2-1-7(10)3-9-14(19)17-16(26)18-15(9)25/h1-4,11-13,20-24H,5-6H2,(H,18,25,26)/t11-,12+,13+/m1/s1
InChIKey 
AUEILLWDYUBWCM-AGIUHOORSA-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
PF00875

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_03293.

PDB 2

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)