Ligand profile

Q5B

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

Bound to: VK055_1793 — succinyl-CoA synthetase, alpha subunit

Via homolog PDB 6z2h UniProt P53396 Formula C₂₇H₄₂N₇O₂₂P₃S
Mol. weight 941.65 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
Q5B
PDB
6z2h
UniProt (similar protein)
P53396
Target protein
VK055_1793

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 941.65 Da
LogP (Crippen) -2.65
H-bond donors 12
H-bond acceptors 22
TPSA 458.46 Ų
Rotatable bonds 24
Aromatic rings 2 / 3
Heavy atoms 60
Fraction sp³ C 0.63
Formula C₂₇H₄₂N₇O₂₂P₃S

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 458.5
  • −1 ≤ LogP ≤ 5 -2.65
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 941.6
  • LogP ≤ 5 -2.65
  • H-bond donors ≤ 5 12
  • H-bond acceptors ≤ 10 22
Veber's rules Fail
  • Rotatable bonds ≤ 10 24
  • TPSA ≤ 140 Ų 458.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCSC(=O)C[C@@](CC(=O)O)(C(=O)O)O)O
InChI 
InChI=1S/C27H42N7O22P3S/c1-26(2,20(40)23(41)30-4-3-14(35)29-5-6-60-16(38)8-27(44,25(42)43)7-15(36)37)10-53-59(50,51)56-58(48,49)52-9-13-19(55-57(45,46)47)18(39)24(54-13)34-12-33-17-21(28)31-11-32-22(17)34/h11-13,18-20,24,39-40,44H,3-10H2,1-2H3,(H,29,35)(H,30,41)(H,36,37)(H,42,43)(H,48,49)(H,50,51)(H2,28,31,32)(H2,45,46,47)/t13-,18-,19-,20+,24-,27+/m1/s1
InChIKey 
IHVFHZGGMJDGGZ-VPXVXCNZSA-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
PF00285

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_1793.

PDB 11

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

Ligand PDB entry

ChEMBL 56

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)