Ligand profile

6CN

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

Bound to: HT085_RS00140 — orotate phosphoribosyltransferase

Via homolog PDB 3ex1 UniProt P11172 Formula C₁₀H₁₂N₃O₉P
Mol. weight 349.19 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6CN
PDB
3ex1
UniProt (similar protein)
P11172
Target protein
HT085_RS00140

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 349.19 Da
LogP (Crippen) -2.86
H-bond donors 5
H-bond acceptors 9
TPSA 195.10 Ų
Rotatable bonds 4
Aromatic rings 1 / 2
Heavy atoms 23
Fraction sp³ C 0.50
Formula C₁₀H₁₂N₃O₉P

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 195.1
  • −1 ≤ LogP ≤ 5 -2.86
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 349.2
  • LogP ≤ 5 -2.86
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 195.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1=C(N(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O)C#N
InChI 
InChI=1S/C10H12N3O9P/c11-2-4-1-6(14)12-10(17)13(4)9-8(16)7(15)5(22-9)3-21-23(18,19)20/h1,5,7-9,15-16H,3H2,(H,12,14,17)(H2,18,19,20)
InChIKey 
GCVKNFUDFHDSJQ-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
PDB
Binding sites
PF00215

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to HT085_RS00140.

PDB 18

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

Ligand PDB entry

ChEMBL 4

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)