Ligand profile

FA2

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

Bound to: KP13_01945 — DNA polymerase II

Via homolog PDB 5vu7 UniProt D0VWU9 Formula C₉H₁₂N₅O₆P
Mol. weight 317.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
FA2
PDB
5vu7
UniProt (similar protein)
D0VWU9
Target protein
KP13_01945

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 317.20 Da
LogP (Crippen) -1.22
H-bond donors 4
H-bond acceptors 9
TPSA 165.84 Ų
Rotatable bonds 3
Aromatic rings 2 / 3
Heavy atoms 21
Fraction sp³ C 0.44
Formula C₉H₁₂N₅O₆P

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 165.8
  • −1 ≤ LogP ≤ 5 -1.22
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 317.2
  • LogP ≤ 5 -1.22
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 165.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H](CO3)OP(=O)(O)O)O)N
InChI 
InChI=1S/C9H12N5O6P/c10-7-5-8(12-2-11-7)14(3-13-5)9-6(15)4(1-19-9)20-21(16,17)18/h2-4,6,9,15H,1H2,(H2,10,11,12)(H2,16,17,18)/t4-,6+,9+/m0/s1
InChIKey 
IJEJRDCFMFEDGL-AFEQZKEHSA-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
PF00136

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_01945.

PDB 13

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)