Ligand profile

1AY

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

Bound to: VK055_2384 — methionine aminopeptidase, type I

Via homolog PDB 4hxx UniProt P53582 Formula C₂₈H₂₉Cl₂N₅
Mol. weight 506.48 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1AY
PDB
4hxx
UniProt (similar protein)
P53582
Target protein
VK055_2384

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 506.48 Da
LogP (Crippen) 6.92
H-bond donors 2
H-bond acceptors 5
TPSA 62.73 Ų
Rotatable bonds 11
Aromatic rings 4 / 4
Heavy atoms 35
Fraction sp³ C 0.25
Formula C₂₈H₂₉Cl₂N₅

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 62.7
  • −1 ≤ LogP ≤ 5 6.92
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 506.5
  • LogP ≤ 5 6.92
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 62.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(nc(n1)c2ccc(cn2)Cl)NC[C@@H](c3ccccc3)NCCCCc4ccccc4)Cl
InChI 
InChI=1S/C28H29Cl2N5/c1-20-26(30)28(35-27(34-20)24-16-15-23(29)18-32-24)33-19-25(22-13-6-3-7-14-22)31-17-9-8-12-21-10-4-2-5-11-21/h2-7,10-11,13-16,18,25,31H,8-9,12,17,19H2,1H3,(H,33,34,35)/t25-/m0/s1
InChIKey 
UZZVALJVPJZKDU-VWLOTQADSA-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)