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Ligand · 3HE

3HE · 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione

3HE, 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione (C15 H23 N O4, 281.4 g/mol), in the MolNFT structures on GenesisL1: bound in 21 records (21 PDB entries). Every binding site with its residues…

Component
3HE
Formula
C15 H23 N O4
Class
ligand
Structures
21
PDB entries
21

Binding sites

3HE in 21 structures; the first of them:

  • 5GAK · Yeast 60S ribosomal subunit with A-site tRNA, P-site tRNA and eIF-5A · 3HE 13401 · binds G92, C93, U2763, C2764, C2765, G2793, G2794, PRO56 and 1 more
  • 5LKS · Structure-function insights reveal the human ribosome as a cancer target for antibiotics · 3HE L55101 · binds G91, C92, U4340, C4341, C4342, G4370, G4371, PRO54 and 1 more
  • 6HD7 · Cryo-EM structure of the ribosome-NatA complex · 3HE 13401 · binds G92, C93, U2763, C2764, C2765, G2793, G2794, PRO56 and 1 more
  • 6TNU · Yeast 80S ribosome in complex with eIF5A and decoding A-site and P-site tRNAs. · 3HE BQ3402 · binds G92, C93, U2763, C2764, C2765, G2793, G2794, LYS55 and 1 more
  • 6Y0G · Structure of human ribosome in classical-PRE state · 3HE L55101 · binds G91, C92, U4340, C4341, C4342, G4370, G4371, LYS53 and 2 more
  • 6Y2L · Structure of human ribosome in POST state · 3HE L55101 · binds G91, C92, U4340, C4341, C4342, G4370, G4371, LYS53 and 1 more
  • 7N8B · Cycloheximide bound vacant 80S structure isolated from cbf5-D95A · 3HE A13401 · binds G92, C93, U2763, C2764, C2765, OMG2793, G2794, LYS55 and 2 more
  • 7Q08 · Structure of Candida albicans 80S ribosome in complex with cycloheximide · 3HE 13402 · binds G91, C92, U2735, C2736, C2737, OMG2765, G2766, MLZ55 and 2 more
  • 7R81 · Structure of the translating Neurospora crassa ribosome arrested by cycloheximide · 3HE A18001 · binds G92, C93, U2723, C2724, C2725, G2753, G2754, LYS55 and 2 more
  • 8BN3 · Yeast 80S, ES7s delta, eIF5A, Stm1 containing · 3HE 13464 · binds G92, C93, U2763, C2764, C2765, G2793, G2794, LYS55 and 2 more
  • 8G6J · mRNA decoding in human is kinetically and structurally distinct from bacteria (GA state 2) · 3HE L55117 · binds G91, C92, U4340, C4341, C4342, OMG4370, G4371, MLZ53 and 3 more
  • 8IPA · Wheat 80S ribosome stalled on AUG-Stop boron dependently with cycloheximide · 3HE RB5197 · binds LYS55, PRO56, G91, C92, U2760, C2761, C2762, G2790 and 1 more
  • 8IPB · Wheat 80S ribosome pausing on AUG-Stop with cycloheximide · 3HE RB5188 · binds LYS55, PRO56, G91, C92, A2759, U2760, C2761, C2762 and 2 more
  • 8T2X · Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, A-site tRNA, messenger… · 3HE A13402 · binds G92, C93, U2763, C2764, C2765, G2793, G2794, LYS55 and 2 more
  • 8T2Y · Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA… · 3HE A13402 · binds G92, C93, U2763, C2764, C2765, G2793, G2794, LYS55 and 2 more
  • 8T2Z · Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA… · 3HE A13402 · binds G92, C93, U2763, C2764, C2765, G2793, G2794, LYS55 and 2 more
  • 8T30 · Hypomethylated yeast 80S bound with cycloheximide, unmodified U2921, mid rotated · 3HE A13402 · binds G92, C93, A2762, U2763, C2764, C2765, G2793, G2794 and 3 more
  • 8UT0 · Eukaryotic 80S ribosome with Reh1, eIF5A and A/P site tRNA · 3HE A3401 · binds G92, C93, A2762, U2763, C2764, C2765, G2793, G2794 and 3 more
  • 8UTI · Eukaryotic 80S ribosome with Reh1 and A/P site tRNA · 3HE A3401 · binds G92, C93, A2762, U2763, C2764, C2765, G2793, G2794 and 3 more
  • 9BH5 · High-resolution C. elegans 80S ribosome structure - class 1 · 3HE A53602 · binds G91, C92, U2875, C2876, C2877, G2905, G2906, LYS54 and 2 more
  • 9CAI · High-resolution C. elegans 80S ribosome structure - class 1 · 3HE A53602 · binds G91, C92, U2875, C2876, C2877, G2905, G2906, LYS54 and 2 more

Residues it binds most

C 21, G 21, U 21, PRO 20, LYS 17, PHE 17, A 4, OMG 3, MLZ 2, GLN 1 (residue and the binding sites it lines).

Found with

  • ZN · Zinc ion
  • SPD · Spermidine
  • MG · Magnesium ion
  • K · Potassium ion
  • GSP · 5'-guanosine-diphosphate-monothiophosphate
  • HMT · (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine
  • MET · Methionine
  • PHE · Phenylalanine
  • PUT · 1,4-diaminobutane
  • YRB · (3R,6R,9S,12S,15S,18S,20R,24aR)-6-[(2S)-butan-2-yl]-3,12-bis[(1R)-1-hydroxy-2-methylpropyl]-8,9,11,17,18-pentamethyl-15-[(2S)-2-methylbutyl]hexadecahydropyrido[1,2-a][1,4,7,10,13,16,19]heptaazacyclohenicosine-1,4,7,10,13,16,19(21H)-heptone

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