Ligand profile

5S4

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

Bound to: VK055_5121 — amino acid adenylation domain protein

Via homolog PDB 5es8 UniProt Q70LM7 Formula C₁₆H₃₃N₄O₈P
Mol. weight 440.43 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5S4
PDB
5es8
UniProt (similar protein)
Q70LM7
Target protein
VK055_5121

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 440.43 Da
LogP (Crippen) -1.80
H-bond donors 7
H-bond acceptors 7
TPSA 200.31 Ų
Rotatable bonds 13
Aromatic rings 0 / 0
Heavy atoms 29
Fraction sp³ C 0.81
Formula C₁₆H₃₃N₄O₈P

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 200.3
  • −1 ≤ LogP ≤ 5 -1.80
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 440.4
  • LogP ≤ 5 -1.80
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 13
  • TPSA ≤ 140 Ų 200.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)[C@@H](C(=O)NCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)O)O)N
InChI 
InChI=1S/C16H33N4O8P/c1-10(2)12(17)14(23)20-8-7-18-11(21)5-6-19-15(24)13(22)16(3,4)9-28-29(25,26)27/h10,12-13,22H,5-9,17H2,1-4H3,(H,18,21)(H,19,24)(H,20,23)(H2,25,26,27)/t12-,13-/m0/s1
InChIKey 
MFHZIFARQCIIMR-STQMWFEESA-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
PF00501' 'PF00550

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_5121.

PDB 14

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 1

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)