Ligand profile

91R

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

Bound to: KP13_00629 — DNA polymerase I

Via homolog PDB 5nkl UniProt P19821 Formula C₁₄H₂₁N₂O₁₆P₃
Mol. weight 566.24 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
91R
PDB
5nkl
UniProt (similar protein)
P19821
Target protein
KP13_00629

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 566.24 Da
LogP (Crippen) -0.52
H-bond donors 7
H-bond acceptors 13
TPSA 277.81 Ų
Rotatable bonds 11
Aromatic rings 1 / 2
Heavy atoms 35
Fraction sp³ C 0.57
Formula C₁₄H₂₁N₂O₁₆P₃

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 277.8
  • −1 ≤ LogP ≤ 5 -0.52
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 566.2
  • LogP ≤ 5 -0.52
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 277.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c(cn(c1[N+](=O)[O-])C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)C#CCC(CO)O
InChI 
InChI=1S/C14H21N2O16P3/c17-7-10(18)3-1-2-9-4-13(16(20)21)15(6-9)14-5-11(19)12(30-14)8-29-34(25,26)32-35(27,28)31-33(22,23)24/h4,6,10-12,14,17-19H,3,5,7-8H2,(H,25,26)(H,27,28)(H2,22,23,24)
InChIKey 
JIVPAQSXWIKFCI-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)