Ligand profile

CHEMBL413376

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_0078 — pyruvate kinase

Via homolog UniProt Q27686 Formula C₅₁H₃₄N₆Na₆O₂₃S₆
pchembl 6.10 ~794.3 nM
Mol. weight 1429.19 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL413376
UniProt (similar protein)
Q27686
pchembl
6.100 (~794.3 nM)
Target protein
VK055_0078

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 1429.19 Da
LogP (Crippen) -13.29
H-bond donors 6
H-bond acceptors 23
TPSA 500.73 Ų
Rotatable bonds 16
Aromatic rings 8 / 8
Heavy atoms 92
Fraction sp³ C 0.04
Formula C₅₁H₃₄N₆Na₆O₂₃S₆

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 500.7
  • −1 ≤ LogP ≤ 5 -13.29
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 1429.2
  • LogP ≤ 5 -13.29
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 23
Veber's rules Fail
  • Rotatable bonds ≤ 10 16
  • TPSA ≤ 140 Ų 500.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ccc(C(=O)Nc2ccc(S(=O)(=O)[O-])c3cc(S(=O)(=O)[O-])cc(S(=O)(=O)[O-])c23)cc1NC(=O)c1cccc(NC(=O)Nc2cccc(C(=O)Nc3cc(C(=O)Nc4ccc(S(=O)(=O)[O-])c5cc(S(=O)(=O)[O-])cc(S(=O)(=O)[O-])c45)ccc3C)c2)c1.[Na+].[Na+].[Na+].[Na+].[Na+].[Na+]
InChI 
InChI=1S/C51H40N6O23S6.6Na/c1-25-9-11-29(49(60)54-37-13-15-41(83(69,70)71)35-21-33(81(63,64)65)23-43(45(35)37)85(75,76)77)19-39(25)56-47(58)27-5-3-7-31(17-27)52-51(62)53-32-8-4-6-28(18-32)48(59)57-40-20-30(12-10-26(40)2)50(61)55-38-14-16-42(84(72,73)74)36-22-34(82(66,67)68)24-44(46(36)38)86(78,79)80;;;;;;/h3-24H,1-2H3,(H,54,60)(H,55,61)(H,56,58)(H,57,59)(H2,52,53,62)(H,63,64,65)(H,66,67,68)(H,69,70,71)(H,72,73,74)(H,75,76,77)(H,78,79,80);;;;;;/q;6*+1/p-6
InChIKey 
VAPNKLKDKUDFHK-UHFFFAOYSA-H

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
ChEMBL
Activity
Inconclusive
Curation
pdb_similarity_tanimoto
Binding sites
PF00224' 'PF02887

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_0078.

PDB 10

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

Ligand PDB entry

ChEMBL 53

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)