Ligand profile

B5X

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

Bound to: VK055_1513 — dihydroorotate dehydrogenase

Via homolog PDB 6j3c UniProt Q02127 Formula C₂₃H₂₄F₂N₄O
Mol. weight 410.47 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
B5X
PDB
6j3c
UniProt (similar protein)
Q02127
Target protein
VK055_1513

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 410.47 Da
LogP (Crippen) 4.68
H-bond donors 0
H-bond acceptors 5
TPSA 51.02 Ų
Rotatable bonds 4
Aromatic rings 3 / 4
Heavy atoms 30
Fraction sp³ C 0.35
Formula C₂₃H₂₄F₂N₄O

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 51.0
  • −1 ≤ LogP ≤ 5 4.68
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 410.5
  • LogP ≤ 5 4.68
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 51.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)[C@@H]1Cc2c(nnn2c3cc(c(c(c3)F)c4cccc(c4)N(C)C)F)C(=O)C1
InChI 
InChI=1S/C23H24F2N4O/c1-13(2)15-9-20-23(21(30)10-15)26-27-29(20)17-11-18(24)22(19(25)12-17)14-6-5-7-16(8-14)28(3)4/h5-8,11-13,15H,9-10H2,1-4H3/t15-/m1/s1
InChIKey 
XGSICBDUCCZAFB-OAHLLOKOSA-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
PF01180

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_1513.

PDB 74

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

Ligand PDB entry

ChEMBL 100

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)