Ligand profile

6MM

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

Bound to: KP13_02055 — Queuine tRNA-ribosyltransferase

Via homolog PDB 5jsw UniProt P28720 Formula C₂₁H₂₆N₆O₆
Mol. weight 458.48 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6MM
PDB
5jsw
UniProt (similar protein)
P28720
Target protein
KP13_02055

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 458.48 Da
LogP (Crippen) 1.19
H-bond donors 4
H-bond acceptors 10
TPSA 158.63 Ų
Rotatable bonds 3
Aromatic rings 3 / 6
Heavy atoms 33
Fraction sp³ C 0.57
Formula C₂₁H₂₆N₆O₆

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 158.6
  • −1 ≤ LogP ≤ 5 1.19
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 458.5
  • LogP ≤ 5 1.19
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 158.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1(OC[C@]2(O1)[C@H]3[C@@H]([C@H](O2)CNc4[nH]c5cc6c(cc5n4)N=C(NC6=O)N)OC(O3)(C)C)C
InChI 
InChI=1S/C21H26N6O6/c1-19(2)29-8-21(33-19)15-14(31-20(3,4)32-15)13(30-21)7-23-18-25-11-5-9-10(6-12(11)26-18)24-17(22)27-16(9)28/h5-6,13-15H,7-8H2,1-4H3,(H2,23,25,26)(H3,22,24,27,28)/t13-,14-,15-,21+/m1/s1
InChIKey 
SAAYEWUENSTOGT-JRMKUOIOSA-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)