Ligand profile

SHX

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

Bound to: VK055_2384 — methionine aminopeptidase, type I

Via homolog PDB 4iku UniProt P53582 Formula C₁₉H₁₈ClN₅O
Mol. weight 367.84 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SHX
PDB
4iku
UniProt (similar protein)
P53582
Target protein
VK055_2384

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 367.84 Da
LogP (Crippen) 3.01
H-bond donors 2
H-bond acceptors 5
TPSA 93.79 Ų
Rotatable bonds 6
Aromatic rings 3 / 3
Heavy atoms 26
Fraction sp³ C 0.16
Formula C₁₉H₁₈ClN₅O

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 93.8
  • −1 ≤ LogP ≤ 5 3.01
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 367.8
  • LogP ≤ 5 3.01
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 93.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(nc(n1)c2ccccn2)N[C@H](Cc3ccccc3)C(=O)N)Cl
InChI 
InChI=1S/C19H18ClN5O/c1-12-16(20)19(25-18(23-12)14-9-5-6-10-22-14)24-15(17(21)26)11-13-7-3-2-4-8-13/h2-10,15H,11H2,1H3,(H2,21,26)(H,23,24,25)/t15-/m1/s1
InChIKey 
SELSGPMCFPHSDG-OAHLLOKOSA-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
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)