Ligand profile

CHEMBL1408293

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_4127 — phosphoglycerate kinase family protein

Via homolog UniProt P07378 Formula C₂₅H₂₄N₆O₈
Mol. weight 536.50 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL1408293
UniProt (similar protein)
P07378
Target protein
VK055_4127

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 536.50 Da
LogP (Crippen) 2.59
H-bond donors 2
H-bond acceptors 9
TPSA 200.37 Ų
Rotatable bonds 7
Aromatic rings 2 / 4
Heavy atoms 39
Fraction sp³ C 0.28
Formula C₂₅H₂₄N₆O₈

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 200.4
  • −1 ≤ LogP ≤ 5 2.59
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 536.5
  • LogP ≤ 5 2.59
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 200.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C=C(C)C(=O)Nc1cccc(C2=NOC3(C2)C[C@@H](C(N)=O)N(C(=O)c2cc([N+](=O)[O-])cc([N+](=O)[O-])c2C)C3)c1
InChI 
InChI=1S/C25H24N6O8/c1-13(2)23(33)27-16-6-4-5-15(7-16)19-10-25(39-28-19)11-21(22(26)32)29(12-25)24(34)18-8-17(30(35)36)9-20(14(18)3)31(37)38/h4-9,21H,1,10-12H2,2-3H3,(H2,26,32)(H,27,33)/t21-,25?/m0/s1
InChIKey 
VRZLMSMBSGRBMV-BWDMCYIDSA-N

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
active
Binding sites
PF00162

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_4127.

PDB 4

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

Ligand PDB entry

ChEMBL 99

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)