Ligand profile

6MQ

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

Bound to: KP13_02055 — Queuine tRNA-ribosyltransferase

Via homolog PDB 5jsv UniProt P28720 Formula C₁₈H₂₂N₆O₅
Mol. weight 402.41 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6MQ
PDB
5jsv
UniProt (similar protein)
P28720
Target protein
KP13_02055

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 402.41 Da
LogP (Crippen) 0.68
H-bond donors 4
H-bond acceptors 9
TPSA 149.40 Ų
Rotatable bonds 4
Aromatic rings 3 / 5
Heavy atoms 29
Fraction sp³ C 0.50
Formula C₁₈H₂₂N₆O₅

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 149.4
  • −1 ≤ LogP ≤ 5 0.68
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 402.4
  • LogP ≤ 5 0.68
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 149.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1(O[C@@H]2[C@H](O[C@H]([C@@H]2O1)OC)CNc3[nH]c4cc5c(cc4n3)C(=O)NC(=N5)N)C
InChI 
InChI=1S/C18H22N6O5/c1-18(2)28-12-11(27-15(26-3)13(12)29-18)6-20-17-22-9-4-7-8(5-10(9)23-17)21-16(19)24-14(7)25/h4-5,11-13,15H,6H2,1-3H3,(H2,20,22,23)(H3,19,21,24,25)/t11-,12-,13-,15-/m1/s1
InChIKey 
DVNDKLBXQGGFSV-RGCMKSIDSA-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
PF01702

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to KP13_02055.

PDB 60

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

Ligand PDB entry

ChEMBL 5

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)