Ligand profile

SVR

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

Bound to: VK055_0078 — pyruvate kinase

Via homolog PDB 3pp7 UniProt Q27686 Formula C₅₁H₄₀N₆O₂₃S₆
Mol. weight 1297.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SVR
PDB
3pp7
UniProt (similar protein)
Q27686
Target protein
VK055_0078

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 1297.30 Da
LogP (Crippen) 6.74
H-bond donors 12
H-bond acceptors 17
TPSA 483.75 Ų
Rotatable bonds 16
Aromatic rings 8 / 8
Heavy atoms 86
Fraction sp³ C 0.04
Formula C₅₁H₄₀N₆O₂₃S₆

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 483.7
  • −1 ≤ LogP ≤ 5 6.74
Lipinski's Rule of Five Fail 4 violations
  • MW ≤ 500 Da 1297.3
  • LogP ≤ 5 6.74
  • H-bond donors ≤ 5 12
  • H-bond acceptors ≤ 10 17
Veber's rules Fail
  • Rotatable bonds ≤ 10 16
  • TPSA ≤ 140 Ų 483.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ccc(cc1NC(=O)c2cccc(c2)NC(=O)Nc3cccc(c3)C(=O)Nc4cc(ccc4C)C(=O)Nc5ccc(c6c5c(cc(c6)S(=O)(=O)O)S(=O)(=O)O)S(=O)(=O)O)C(=O)Nc7ccc(c8c7c(cc(c8)S(=O)(=O)O)S(=O)(=O)O)S(=O)(=O)O
InChI 
InChI=1S/C51H40N6O23S6/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)
InChIKey 
FIAFUQMPZJWCLV-UHFFFAOYSA-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
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 9

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

Ligand PDB entry

ChEMBL 54

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)