Ligand profile

DCS

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

Bound to: KP13_01696 — Lipopolysaccharide biosynthesis protein rffA

Via homolog PDB 1mdz UniProt Q8ZNF3 Formula C₁₁H₁₆N₃O₇P
Mol. weight 333.24 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DCS
PDB
1mdz
UniProt (similar protein)
Q8ZNF3
Target protein
KP13_01696

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 333.24 Da
LogP (Crippen) -0.78
H-bond donors 5
H-bond acceptors 7
TPSA 150.24 Ų
Rotatable bonds 6
Aromatic rings 1 / 2
Heavy atoms 22
Fraction sp³ C 0.45
Formula C₁₁H₁₆N₃O₇P

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 150.2
  • −1 ≤ LogP ≤ 5 -0.78
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 333.2
  • LogP ≤ 5 -0.78
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 150.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H]2CONC2=O)O
InChI 
InChI=1S/C11H16N3O7P/c1-6-10(15)8(3-13-9-5-20-14-11(9)16)7(2-12-6)4-21-22(17,18)19/h2,9,13,15H,3-5H2,1H3,(H,14,16)(H2,17,18,19)/t9-/m1/s1
InChIKey 
NNRZSZJOQKAGTO-SECBINFHSA-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
PF01041

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_01696.

PDB 7

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)