Ligand profile

DG9

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

Bound to: VK055_5121 — amino acid adenylation domain protein

Via homolog PDB 6mg0 UniProt Q70LM7 Formula C₂₇H₄₈N₉O₁₂PS₂
Mol. weight 785.84 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DG9
PDB
6mg0
UniProt (similar protein)
Q70LM7
Target protein
VK055_5121

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 785.84 Da
LogP (Crippen) -2.85
H-bond donors 10
H-bond acceptors 17
TPSA 336.69 Ų
Rotatable bonds 20
Aromatic rings 2 / 3
Heavy atoms 51
Fraction sp³ C 0.74
Formula C₂₇H₄₈N₉O₁₂PS₂

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 336.7
  • −1 ≤ LogP ≤ 5 -2.85
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 785.8
  • LogP ≤ 5 -2.85
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 17
Veber's rules Fail
  • Rotatable bonds ≤ 10 20
  • TPSA ≤ 140 Ų 336.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)[C@H]([C@H](CS(=O)(=O)NC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)O)O)N
InChI 
InChI=1S/C27H48N9O12PS2/c1-14(2)18(28)16(50-8-7-30-17(37)5-6-31-25(41)22(40)27(3,4)11-47-49(42,43)44)10-51(45,46)35-9-15-20(38)21(39)26(48-15)36-13-34-19-23(29)32-12-33-24(19)36/h12-16,18,20-22,26,35,38-40H,5-11,28H2,1-4H3,(H,30,37)(H,31,41)(H2,29,32,33)(H2,42,43,44)/t15-,16+,18-,20-,21-,22+,26-/m1/s1
InChIKey 
LAWRAYXGFUHBCH-AWSFPXBRSA-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)