Ligand profile

9DI

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

Bound to: VK055_0519 — adenosine deaminase

Via homolog PDB 3km8 UniProt P03958 Formula C₁₁H₁₃N₃O₅
Mol. weight 267.24 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9DI
PDB
3km8
UniProt (similar protein)
P03958
Target protein
VK055_0519

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 267.24 Da
LogP (Crippen) -1.59
H-bond donors 5
H-bond acceptors 6
TPSA 131.46 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 19
Fraction sp³ C 0.45
Formula C₁₁H₁₃N₃O₅

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 131.5
  • −1 ≤ LogP ≤ 5 -1.59
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 267.2
  • LogP ≤ 5 -1.59
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 131.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c(c2c([nH]1)C(=O)NC=N2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O
InChI 
InChI=1S/C11H13N3O5/c15-2-5-8(16)9(17)10(19-5)4-1-12-7-6(4)13-3-14-11(7)18/h1,3,5,8-10,12,15-17H,2H2,(H,13,14,18)/t5-,8-,9-,10+/m1/s1
InChIKey 
WKDMPDYUJKSXBW-KBHCAIDQSA-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
PF00962

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_0519.

PDB 11

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

Ligand PDB entry

ChEMBL 100

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)