Ligand profile

CHEMBL1627105

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_5117 — 2,3-dihydroxybenzoate-AMP ligase

Via homolog UniProt P71716 Formula C₂₉H₂₅N₆NaO₈S
pchembl 8.85 ~1.4 nM
Mol. weight 640.61 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL1627105
UniProt (similar protein)
P71716
pchembl
8.850 (~1.4 nM)
Target protein
VK055_5117

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 640.61 Da
LogP (Crippen) -0.45
H-bond donors 4
H-bond acceptors 13
TPSA 214.08 Ų
Rotatable bonds 8
Aromatic rings 5 / 6
Heavy atoms 45
Fraction sp³ C 0.17
Formula C₂₉H₂₅N₆NaO₈S

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 214.1
  • −1 ≤ LogP ≤ 5 -0.45
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 640.6
  • LogP ≤ 5 -0.45
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 214.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1nc(-c2cccc(-c3ccccc3)c2)nc2c1ncn2[C@@H]1O[C@H](COS(=O)(=O)[N-]C(=O)c2ccccc2O)[C@@H](O)[C@H]1O.[Na+]
InChI 
InChI=1S/C29H26N6O8S.Na/c30-25-22-27(33-26(32-25)18-10-6-9-17(13-18)16-7-2-1-3-8-16)35(15-31-22)29-24(38)23(37)21(43-29)14-42-44(40,41)34-28(39)19-11-4-5-12-20(19)36;/h1-13,15,21,23-24,29,37-38H,14H2,(H4,30,32,33,34,36,39);/q;+1/p-1/t21-,23-,24-,29-;/m1./s1
InChIKey 
QBGAEYQOIMOWDV-HMPRVOSNSA-M

Provenance

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

Method
LigQ nearest_k
Source
ChEMBL
Curation
pdb_similarity_tanimoto
Binding sites
PF00501' 'PF13193

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_5117.

PDB 7

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

Ligand PDB entry

ChEMBL 81

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)