Ligand profile

HHZ

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

Bound to: KP13_00629 — DNA polymerase I

Via homolog PDB 6q4u UniProt P19821 Formula C₁₈H₂₆N₅O₁₅P₃
Mol. weight 645.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HHZ
PDB
6q4u
UniProt (similar protein)
P19821
Target protein
KP13_00629

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 645.35 Da
LogP (Crippen) -1.52
H-bond donors 8
H-bond acceptors 15
TPSA 304.57 Ų
Rotatable bonds 13
Aromatic rings 2 / 3
Heavy atoms 41
Fraction sp³ C 0.50
Formula C₁₈H₂₆N₅O₁₅P₃

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 304.6
  • −1 ≤ LogP ≤ 5 -1.52
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 645.3
  • LogP ≤ 5 -1.52
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 15
Veber's rules Fail
  • Rotatable bonds ≤ 10 13
  • TPSA ≤ 140 Ų 304.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c(c2c(ncnc2n1C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N)C#CCNC(=O)COCCO
InChI 
InChI=1S/C18H26N5O15P3/c19-17-16-11(2-1-3-20-14(26)9-34-5-4-24)7-23(18(16)22-10-21-17)15-6-12(25)13(36-15)8-35-40(30,31)38-41(32,33)37-39(27,28)29/h7,10,12-13,15,24-25H,3-6,8-9H2,(H,20,26)(H,30,31)(H,32,33)(H2,19,21,22)(H2,27,28,29)
InChIKey 
FDFHIISDJKYZQH-UHFFFAOYSA-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
PF00476

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_00629.

PDB 34

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)