Ligand profile

U11

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

Bound to: VK055_2384 — methionine aminopeptidase, type I

Via homolog PDB 2gg0 UniProt P0AE18 Formula C₁₆H₂₀F₃N₃O₅
Mol. weight 391.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
U11
PDB
2gg0
UniProt (similar protein)
P0AE18
Target protein
VK055_2384

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 391.35 Da
LogP (Crippen) -0.14
H-bond donors 4
H-bond acceptors 6
TPSA 130.75 Ų
Rotatable bonds 7
Aromatic rings 1 / 1
Heavy atoms 27
Fraction sp³ C 0.44
Formula C₁₆H₂₀F₃N₃O₅

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 130.8
  • −1 ≤ LogP ≤ 5 -0.14
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 391.3
  • LogP ≤ 5 -0.14
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 130.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H](C(=O)NCC(=O)OC)NC(=O)[C@H]([C@@H](c1ccc(cc1)C(F)(F)F)N)O
InChI 
InChI=1S/C16H20F3N3O5/c1-8(14(25)21-7-11(23)27-2)22-15(26)13(24)12(20)9-3-5-10(6-4-9)16(17,18)19/h3-6,8,12-13,24H,7,20H2,1-2H3,(H,21,25)(H,22,26)/t8-,12+,13-/m0/s1
InChIKey 
KTNRONBAQGRLNO-CKLFPEKLSA-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
PF00557

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_2384.

PDB 45

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)