Ligand profile

0R5

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

Bound to: KP13_00629 — DNA polymerase I

Via homolog PDB 4elt UniProt P19821 Formula C₁₉H₁₉N₂O₁₄P₃
Mol. weight 592.28 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
0R5
PDB
4elt
UniProt (similar protein)
P19821
Target protein
KP13_00629

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 592.28 Da
LogP (Crippen) -0.09
H-bond donors 6
H-bond acceptors 11
TPSA 244.14 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 38
Fraction sp³ C 0.26
Formula C₁₉H₁₉N₂O₁₄P₃

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 244.1
  • −1 ≤ LogP ≤ 5 -0.09
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 592.3
  • LogP ≤ 5 -0.09
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 244.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C#Cc1ccc(cc1)C#CC2=CN(C(=O)NC2=O)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
InChI 
InChI=1S/C19H19N2O14P3/c1-2-12-3-5-13(6-4-12)7-8-14-10-21(19(24)20-18(14)23)17-9-15(22)16(33-17)11-32-37(28,29)35-38(30,31)34-36(25,26)27/h1,3-6,10,15-17,22H,9,11H2,(H,28,29)(H,30,31)(H,20,23,24)(H2,25,26,27)
InChIKey 
NDHYKBWELLKQHS-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)