Ligand profile

9BX

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

Bound to: VK055_1513 — dihydroorotate dehydrogenase

Via homolog PDB 5zfb UniProt Q02127 Formula C₂₃H₂₉ClO₅
Mol. weight 420.93 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9BX
PDB
5zfb
UniProt (similar protein)
Q02127
Target protein
VK055_1513

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 420.93 Da
LogP (Crippen) 4.98
H-bond donors 3
H-bond acceptors 5
TPSA 94.83 Ų
Rotatable bonds 9
Aromatic rings 1 / 1
Heavy atoms 29
Fraction sp³ C 0.39
Formula C₂₃H₂₉ClO₅

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 94.8
  • −1 ≤ LogP ≤ 5 4.98
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 420.9
  • LogP ≤ 5 4.98
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 94.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c(c(c1Cl)O)C/C=C(/C)\CC/C=C(/C)\C=C\C(=O)C(C)(C)O)O)C=O
InChI 
InChI=1S/C23H29ClO5/c1-14(7-6-8-15(2)10-12-19(26)23(4,5)29)9-11-17-21(27)18(13-25)16(3)20(24)22(17)28/h8-10,12-13,27-29H,6-7,11H2,1-5H3/b12-10+,14-9-,15-8-
InChIKey 
NCZOBEWCFSMGDM-ZTAYFTFOSA-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)