Ligand profile

Q06

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

Bound to: VK055_2384 — methionine aminopeptidase, type I

Via homolog PDB 4u6c UniProt P53582 Formula C₈H₁₈NO₃P
Mol. weight 207.21 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
Q06
PDB
4u6c
UniProt (similar protein)
P53582
Target protein
VK055_2384

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 207.21 Da
LogP (Crippen) 1.42
H-bond donors 3
H-bond acceptors 2
TPSA 83.55 Ų
Rotatable bonds 4
Aromatic rings 0 / 1
Heavy atoms 13
Fraction sp³ C 1.00
Formula C₈H₁₈NO₃P

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 83.6
  • −1 ≤ LogP ≤ 5 1.42
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 207.2
  • LogP ≤ 5 1.42
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 83.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1CCC(C1)CC[C@H](N)P(=O)(O)O
InChI 
InChI=1S/C8H18NO3P/c9-8(13(10,11)12)6-5-7-3-1-2-4-7/h7-8H,1-6,9H2,(H2,10,11,12)/t8-/m1/s1
InChIKey 
ZLDKOVICXZHRSD-MRVPVSSYSA-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)