Ligand profile

CHEMBL4859176

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_0072 — holliday junction DNA helicase RuvB

Via homolog UniProt P55072 Formula C₂₉H₂₈BN₅O₄

pchembl 7.03 ~93.3 nM

Mol. weight 521.39 Da

Permeability Check

PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID: CHEMBL4859176
UniProt (similar protein): P55072
pchembl: 7.030 (~93.3 nM)
Target protein: VK055_0072

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 521.39 Da

LogP (Crippen) 3.74

H-bond donors 4

H-bond acceptors 8

TPSA 125.44 Å²

Rotatable bonds 7

Aromatic rings 5 / 6

Heavy atoms 39

Fraction sp³ C 0.21

Formula C₂₉H₂₈BN₅O₄

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 Å² and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

TPSA ≤ 90 Å² 125.4
−1 ≤ LogP ≤ 5 3.74

Lipinski's Rule of Five Pass 1 violation

MW ≤ 500 Da 521.4
LogP ≤ 5 3.74
H-bond donors ≤ 5 4
H-bond acceptors ≤ 10 8

Veber's rules Pass

Rotatable bonds ≤ 10 7
TPSA ≤ 140 Å² 125.4

PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES

Cc1cc2c(NC(=O)c3ccco3)cccc2n1-c1nc2c(c(NCc3cccc(B(O)O)c3)n1)CCCC2

InChI

InChI=1S/C29H28BN5O4/c1-18-15-22-24(32-28(36)26-13-6-14-39-26)11-5-12-25(22)35(18)29-33-23-10-3-2-9-21(23)27(34-29)31-17-19-7-4-8-20(16-19)30(37)38/h4-8,11-16,37-38H,2-3,9-10,17H2,1H3,(H,32,36)(H,31,33,34)

InChIKey

RGRLEBDKWGUCPT-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: ChEMBL
Curation: pdb_similarity_tanimoto
Binding sites: PF00004' 'PF17862

External resources

Open this ligand in third-party databases and cheminformatics tools.

ChEMBL ChEMBL compound CHEMBL4859176 →
UniProt UniProt P55072 (homolog) →
PubChem PubChem (by InChIKey) →
Cheminformatics SwissADME prediction →
Cheminformatics SwissTargetPrediction →
Web Google Scholar (search “CHEMBL4859176”) →

Other ligands for this protein

Quick navigation to other ligands bound to VK055_0072.

PDB 9

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)