Ligand profile

DCT

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

Bound to: KP13_00629 — DNA polymerase I

Via homolog PDB 6vdd UniProt A0QYZ2 Formula C₉H₁₆N₃O₁₂P₃
Mol. weight 451.16 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DCT
PDB
6vdd
UniProt (similar protein)
A0QYZ2
Target protein
KP13_00629

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 451.16 Da
LogP (Crippen) -0.15
H-bond donors 5
H-bond acceptors 11
TPSA 229.96 Ų
Rotatable bonds 8
Aromatic rings 1 / 2
Heavy atoms 27
Fraction sp³ C 0.56
Formula C₉H₁₆N₃O₁₂P₃

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 230.0
  • −1 ≤ LogP ≤ 5 -0.15
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 451.2
  • LogP ≤ 5 -0.15
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 230.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1C[C@@H](O[C@@H]1CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)N2C=CC(=NC2=O)N
InChI 
InChI=1S/C9H16N3O12P3/c10-7-3-4-12(9(13)11-7)8-2-1-6(22-8)5-21-26(17,18)24-27(19,20)23-25(14,15)16/h3-4,6,8H,1-2,5H2,(H,17,18)(H,19,20)(H2,10,11,13)(H2,14,15,16)/t6-,8+/m0/s1
InChIKey 
ARLKCWCREKRROD-POYBYMJQSA-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)