Ligand profile

DDY

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

Bound to: KP13_32224 — DNA polymerase IV

Via homolog PDB 1s9f UniProt Q97W02 Formula C₉H₁₅N₃O₉P₂
Mol. weight 371.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DDY
PDB
1s9f
UniProt (similar protein)
Q97W02
Target protein
KP13_32224

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 371.18 Da
LogP (Crippen) -0.27
H-bond donors 4
H-bond acceptors 9
TPSA 183.43 Ų
Rotatable bonds 6
Aromatic rings 1 / 2
Heavy atoms 23
Fraction sp³ C 0.56
Formula C₉H₁₅N₃O₉P₂

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 183.4
  • −1 ≤ LogP ≤ 5 -0.27
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 371.2
  • LogP ≤ 5 -0.27
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 183.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1C[C@@H](O[C@@H]1CO[P@@](=O)(O)OP(=O)(O)O)N2C=CC(=NC2=O)N
InChI 
InChI=1S/C9H15N3O9P2/c10-7-3-4-12(9(13)11-7)8-2-1-6(20-8)5-19-23(17,18)21-22(14,15)16/h3-4,6,8H,1-2,5H2,(H,17,18)(H2,10,11,13)(H2,14,15,16)/t6-,8+/m0/s1
InChIKey 
FVSQWXITYSICAK-POYBYMJQSA-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)