Ligand profile

RLP

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

Bound to: VK055_2187 — 6,7-dimethyl-8-ribityllumazine synthase

Via homolog PDB 1nqx UniProt O66529 Formula C₁₄H₁₈N₄O₉
Mol. weight 386.32 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
RLP
PDB
1nqx
UniProt (similar protein)
O66529
Target protein
VK055_2187

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 386.32 Da
LogP (Crippen) -3.77
H-bond donors 7
H-bond acceptors 11
TPSA 219.09 Ų
Rotatable bonds 8
Aromatic rings 0 / 2
Heavy atoms 27
Fraction sp³ C 0.50
Formula C₁₄H₁₈N₄O₉

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 219.1
  • −1 ≤ LogP ≤ 5 -3.77
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 386.3
  • LogP ≤ 5 -3.77
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 219.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CC(=O)O)C1=C(N(C2=NC(=O)NC(=O)C2=N1)C[C@@H]([C@@H]([C@@H](CO)O)O)O)O
InChI 
InChI=1S/C14H18N4O9/c19-4-7(21)10(24)6(20)3-18-11-9(12(25)17-14(27)16-11)15-5(13(18)26)1-2-8(22)23/h6-7,10,19-21,24,26H,1-4H2,(H,22,23)(H,17,25,27)/t6-,7+,10-/m0/s1
InChIKey 
ZUXCIPRCLKZSHS-PJKMHFRUSA-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
PF00885

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_2187.

PDB 7

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

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)