Ligand profile

ST9

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

Bound to: VK055_2882 — aidB

Via homolog PDB 6ksa UniProt Q3L887 Formula C₃₉H₇₀N₇O₁₇P₃S
Mol. weight 1034.01 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ST9
PDB
6ksa
UniProt (similar protein)
Q3L887
Target protein
VK055_2882

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 1034.01 Da
LogP (Crippen) 4.93
H-bond donors 9
H-bond acceptors 19
TPSA 363.63 Ų
Rotatable bonds 35
Aromatic rings 2 / 3
Heavy atoms 67
Fraction sp³ C 0.79
Formula C₃₉H₇₀N₇O₁₇P₃S

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 363.6
  • −1 ≤ LogP ≤ 5 4.93
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 1034.0
  • LogP ≤ 5 4.93
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 19
Veber's rules Fail
  • Rotatable bonds ≤ 10 35
  • TPSA ≤ 140 Ų 363.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
InChI 
InChI=1S/C39H70N7O17P3S/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-30(48)67-23-22-41-29(47)20-21-42-37(51)34(50)39(2,3)25-60-66(57,58)63-65(55,56)59-24-28-33(62-64(52,53)54)32(49)38(61-28)46-27-45-31-35(40)43-26-44-36(31)46/h26-28,32-34,38,49-50H,4-25H2,1-3H3,(H,41,47)(H,42,51)(H,55,56)(H,57,58)(H2,40,43,44)(H2,52,53,54)/t28-,32-,33-,34+,38-/m1/s1
InChIKey 
SIARJEKBADXQJG-LFZQUHGESA-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
PF00441' 'PF02770

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_2882.

PDB 14

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

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)