Ligand profile

DOC

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

Bound to: KP13_31499 — Cytidylate kinase

Via homolog PDB 1kdt UniProt P0A6I0 Formula C₉H₁₄N₃O₆P
Mol. weight 291.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DOC
PDB
1kdt
UniProt (similar protein)
P0A6I0
Target protein
KP13_31499

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 291.20 Da
LogP (Crippen) -0.39
H-bond donors 3
H-bond acceptors 7
TPSA 136.90 Ų
Rotatable bonds 4
Aromatic rings 1 / 2
Heavy atoms 19
Fraction sp³ C 0.56
Formula C₉H₁₄N₃O₆P

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 136.9
  • −1 ≤ LogP ≤ 5 -0.39
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 291.2
  • LogP ≤ 5 -0.39
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 136.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1C[C@@H](O[C@@H]1COP(=O)(O)O)N2C=CC(=NC2=O)N
InChI 
InChI=1S/C9H14N3O6P/c10-7-3-4-12(9(13)11-7)8-2-1-6(18-8)5-17-19(14,15)16/h3-4,6,8H,1-2,5H2,(H2,10,11,13)(H2,14,15,16)/t6-,8+/m0/s1
InChIKey 
RAJMXAZJKUGYGW-POYBYMJQSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF02224

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_31499.

PDB 2

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)