Ligand profile

YYY

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

Bound to: KP13_32224 — DNA polymerase IV

Via homolog PDB 4qwb UniProt Q97W02 Formula C₉H₁₅N₃O₁₀P₂
Mol. weight 387.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
YYY
PDB
4qwb
UniProt (similar protein)
Q97W02
Target protein
KP13_32224

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 387.18 Da
LogP (Crippen) -1.30
H-bond donors 5
H-bond acceptors 10
TPSA 203.66 Ų
Rotatable bonds 6
Aromatic rings 1 / 2
Heavy atoms 24
Fraction sp³ C 0.56
Formula C₉H₁₅N₃O₁₀P₂

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 203.7
  • −1 ≤ LogP ≤ 5 -1.30
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 387.2
  • LogP ≤ 5 -1.30
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 203.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO[P@@](=O)(O)OP(=O)(O)O)O
InChI 
InChI=1S/C9H15N3O10P2/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(21-8)4-20-24(18,19)22-23(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
InChIKey 
FTDHDKPUHBLBTL-SHYZEUOFSA-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
PF00817

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_32224.

PDB 31

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 3

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)