Ligand profile

DDS

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

Bound to: KP13_00629 — DNA polymerase I

Via homolog PDB 1qsy UniProt P19821 Formula C₁₀H₁₆N₅O₁₁P₃
Mol. weight 475.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DDS
PDB
1qsy
UniProt (similar protein)
P19821
Target protein
KP13_00629

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 475.18 Da
LogP (Crippen) 0.43
H-bond donors 5
H-bond acceptors 12
TPSA 238.67 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 29
Fraction sp³ C 0.50
Formula C₁₀H₁₆N₅O₁₁P₃

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 238.7
  • −1 ≤ LogP ≤ 5 0.43
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 475.2
  • LogP ≤ 5 0.43
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 238.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)[C@H]3CC[C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)N
InChI 
InChI=1S/C10H16N5O11P3/c11-9-8-10(13-4-12-9)15(5-14-8)7-2-1-6(24-7)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h4-7H,1-3H2,(H,19,20)(H,21,22)(H2,11,12,13)(H2,16,17,18)/t6-,7+/m0/s1
InChIKey 
OAKPWEUQDVLTCN-NKWVEPMBSA-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)