Ligand profile

MLN

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

Bound to: VK055_3786 — peptide deformylase

Via homolog PDB 1bsj UniProt P0A6K3 Formula C₁₈H₂₈N₃O₈P
Mol. weight 445.41 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
MLN
PDB
1bsj
UniProt (similar protein)
P0A6K3
Target protein
VK055_3786

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 445.41 Da
LogP (Crippen) 2.73
H-bond donors 4
H-bond acceptors 6
TPSA 168.10 Ų
Rotatable bonds 12
Aromatic rings 1 / 1
Heavy atoms 30
Fraction sp³ C 0.56
Formula C₁₈H₂₈N₃O₈P

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 168.1
  • −1 ≤ LogP ≤ 5 2.73
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 445.4
  • LogP ≤ 5 2.73
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 168.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCC[C@@H](C(=O)N[C@@H](CC(C)C)C(=O)Nc1ccc(cc1)[N+](=O)[O-])OP(=O)(O)O
InChI 
InChI=1S/C18H28N3O8P/c1-4-5-6-16(29-30(26,27)28)18(23)20-15(11-12(2)3)17(22)19-13-7-9-14(10-8-13)21(24)25/h7-10,12,15-16H,4-6,11H2,1-3H3,(H,19,22)(H,20,23)(H2,26,27,28)/t15-,16-/m0/s1
InChIKey 
HARXAJAHMRMERT-HOTGVXAUSA-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
PF01327

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_3786.

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)