UniProt Q8IXJ6
NAD-dependent protein deacetylase sirtuin-2 (Q8IXJ6)
NAD-dependent protein deacetylase sirtuin-2 (UniProt Q8IXJ6), EC 2.3.1.-, 2.3.1.286: 86 experimental structures and 1 predicted model on GenesisL1, 39 ligands bound, 115 pockets. Binding sites, druggability and experiment against…
- UniProt
- Q8IXJ6
- Protein
- NAD-dependent protein deacetylase sirtuin-2
- EC
- 2.3.1.-, 2.3.1.286, 3.5.1.-
- Experimental structures
- 86
- Predicted models
- 1
- Ligands
- 39
- Pockets
- 115 · 30 records with a druggable one
Structures
87 records of Q8IXJ6 in the MolNFT archive: 86 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 1J8F | Human SIRT2 histone deacetylase | x-ray diffraction | A, B, C | ZN | 14 (best 0.64) |
| 1J8F | Human SIRT2 histone deacetylase | x-ray diffraction | A, B, C | — | — |
| 3ZGO | Re-refined structure of the human Sirt2 apoform | x-ray diffraction | A, B, C | — | — |
| 3ZGO | Re-refined structure of the human SIRT2 apoform | x-ray diffraction | A, B, C | — | — |
| 3ZGV | Structure of human SIRT2 in complex with ADP-ribose | x-ray diffraction | A, B | — | — |
| 3ZGV | Structure of human SIRT2 in complex with ADP-ribose | x-ray diffraction | A, B | — | — |
| 4L3O | Crystal Structure of SIRT2 in complex with the macrocyclic peptide S2iL5 | x-ray diffraction | A, B, C, D | — | — |
| 4L3O | Crystal structure of SIRT2 in complex with the macrocyclic peptide S2IL5 | x-ray diffraction | A, B, C, D | — | — |
| 4R8M | Human SIRT2 crystal structure in complex with BHJH-TM1 | x-ray diffraction | A, B | — | — |
| 4R8M | Human SIRT2 crystal structure in complex with bhjh-TM1 | x-ray diffraction | A, B | — | — |
| 4RMG | Human Sirt2 in complex with SirReal2 and NAD+ | x-ray diffraction | A | — | — |
| 4RMG | Human SIRT2 in complex with SIRREAL2 and NAD+ | x-ray diffraction | A | — | — |
| 4RMH | Human Sirt2 in complex with SirReal2 and Ac-Lys-H3 peptide | x-ray diffraction | A | — | — |
| 4RMH | Human SIRT2 in complex with SIRREAL2 and ac-lys-H3 peptide | x-ray diffraction | A | — | — |
| 4RMI | Human Sirt2 in complex with SirReal1 and Ac-Lys-OTC peptide | x-ray diffraction | A | — | — |
| 4RMI | Human SIRT2 in complex with SIRREAL1 and ac-lys-otc peptide | x-ray diffraction | A | — | — |
| 4RMJ | Human Sirt2 in complex with ADP ribose and nicotinamide | x-ray diffraction | A, B | — | — |
| 4RMJ | Human SIRT2 in complex with ADP ribose and nicotinamide | x-ray diffraction | A, B | — | — |
| 4X3O | Sirt2 in complex with a myristoyl peptide | x-ray diffraction | A | — | — |
| 4X3O | SIRT2 in complex with a myristoyl peptide | x-ray diffraction | A | — | — |
| 4X3P | Sirt2 in complex with a myristoyl peptide | x-ray diffraction | A | — | — |
| 4X3P | SIRT2 in complex with a myristoyl peptide | x-ray diffraction | A | — | — |
| 4Y6L | Human SIRT2 in complex with myristoylated peptide (H3K9myr) | x-ray diffraction | A, B | — | — |
| 4Y6L | Human SIRT2 in complex with myristoylated peptide (H3K9MYR) | x-ray diffraction | A, B | — | — |
| 4Y6O | Human SIRT2 in complex with myristoylated peptide (TNF-alphaK20myr) | x-ray diffraction | A, B | — | — |
| 4Y6O | Human SIRT2 in complex with myristoylated peptide (TNF-ALPHAK20MYR) | x-ray diffraction | A, B | — | — |
| 4Y6Q | Human SIRT2 in complex with 2-O-myristoyl-ADP-ribose | x-ray diffraction | A, B, C, D | — | — |
| 4Y6Q | Human SIRT2 in complex with 2-O-myristoyl-ADP-ribose | x-ray diffraction | A, B, C, D | — | — |
| 5D7O | Crystal structure of Sirt2-ADPR at an improved resolution | x-ray diffraction | A, B | ZN, AR6 | 6 (best 0.79) |
| 5D7O | Crystal structure of SIRT2-adpr at an improved resolution | x-ray diffraction | A, B | — | — |
| 5D7P | Crystal structure of human Sirt2 in complex with ADPR and EX-243 | x-ray diffraction | A, B | ZN, AR6, OCZ | 7 (best 0.83) |
| 5D7P | Crystal structure of human SIRT2 in complex with adpr and ex-243 | x-ray diffraction | A, B | — | — |
| 5D7Q | Crystal structure of human SIRT2 in complex with adpr and CHIC35 | x-ray diffraction | A, B | — | — |
| 5DY4 | Crystal structure of human Sirt2 in complex with a brominated 2nd generation SirReal inhibitor and… | x-ray diffraction | A | ZN, 5GN, NAD | — |
| 5DY4 | Crystal structure of human SIRT2 in complex with a brominated 2ND generation sirreal inhibitor and… | x-ray diffraction | A | — | — |
| 5DY5 | Crystal structure of human Sirt2 in complex with a SirReal probe fragment | x-ray diffraction | A | ZN, 5GR | — |
| 5DY5 | Crystal structure of human SIRT2 in complex with a sirreal probe fragment | x-ray diffraction | A | — | — |
| 5FYQ | Sirt2 in complex with a 13-mer trifluoroacetylated Ran peptide | x-ray diffraction | A, B | SO4, ZN | 7 (best 0.74) |
| 5FYQ | SIRT2 in complex with a 13-mer trifluoroacetylated ran peptide | x-ray diffraction | A, B | — | — |
| 5G4C | Human SIRT2 catalyse short chain fatty acyl lysine | x-ray diffraction | A, B | ZN, CNA | — |
| 5G4C | Human SIRT2 catalyse short chain fatty acyl lysine | x-ray diffraction | A, B | — | — |
| 5MAR | Structure of human SIRT2 in complex with 1,2,4-Oxadiazole inhibitor and ADP ribose. | x-ray diffraction | A, B | ZN, AR6, 7KE | 7 (best 0.82) |
| 5MAR | Structure of human SIRT2 in complex with 1,2,4-oxadiazole inhibitor and ADP ribose. | x-ray diffraction | A, B | ZN, AR6, 7KE | — |
| 5MAT | Structure of human Sirtuin 2 in complex with a selective thienopyrimidi based inhibitor | x-ray diffraction | A, C | ZN, 7KJ, SO4 | 6 (best 0.81) |
| 5MAT | Structure of human sirtuin 2 in complex with a selective thienopyrimidinone based inhibitor | x-ray diffraction | A, C | ZN, 7KJ, SO4 | — |
| 5Y0Z | Human SIRT2 in complex with a specific inhibitor, NPD11033 | x-ray diffraction | A, B | ZN, 8K9 | 7 (best 0.83) |
| 5Y0Z | Human SIRT2 in complex with a specific inhibitor, NPD11033 | x-ray diffraction | A, B | ZN, 8K9 | — |
| 5Y5N | Crystal structure of human Sirtuin 2 in complex with a selective inhibitor | x-ray diffraction | A | ZN, 8NO | 2 (best 0.76) |
| 5Y5N | Crystal structure of human sirtuin 2 in complex with a selective inhibitor | x-ray diffraction | A | ZN, 8NO | — |
| 5YQL | Crystal structure of Sirt2 in complex with selective inhibitor A2I | x-ray diffraction | A | A2I, ZN | 3 (best 0.77) |
| 5YQL | Crystal structure of SIRT2 in complex with selective inhibitor A2I | x-ray diffraction | A | A2I, ZN | — |
| 5YQM | Crystal structure of Sirt2 in complex with selective inhibitor A29 | x-ray diffraction | A | ZN, A2X | 2 (best 0.78) |
| 5YQM | Crystal structure of SIRT2 in complex with selective inhibitor A29 | x-ray diffraction | A | ZN, A2X | — |
| 5YQN | Crystal structure of Sirt2 in complex with selective inhibitor L55 | x-ray diffraction | A | ZN, L55 | 2 (best 0.77) |
| 5YQN | Crystal structure of SIRT2 in complex with selective inhibitor L55 | x-ray diffraction | A | ZN, L55 | — |
| 5YQO | Crystal structure of Sirt2 in complex with selective inhibitor L5C | x-ray diffraction | A | ZN, L5C | — |
| 5YQO | Crystal structure of SIRT2 in complex with selective inhibitor L5C | x-ray diffraction | A | ZN, L5C | — |
| 6L65 | Sirtuin 2 protein with H3K18 myristoylated peptide | x-ray diffraction | A | ZN, MYR | 3 (best 0.81) |
| 6L65 | Sirtuin 2 protein with H3K18 myristoylated peptide | x-ray diffraction | A | ZN, MYR | — |
| 6L66 | Sirtuin 2 protein with H3K18 myristoylated peptide and intact NAD molecule | x-ray diffraction | A | ZN, NAD, 3LX | — |
27 records more on the page itself.
Ligands
- ZN · Zinc ion · in 50 records
- AR6 · [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2R,3S,4R,5S)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate · in 6 records
- NAD · Nicotinamide-adenine-dinucleotide · in 6 records
- SO4 · Sulfate ion · in 6 records
- F4R · N-dodecylmethanethioamide · in 4 records
- MYR · Myristic acid · in 3 records
- 3LX · tridecanethial · in 2 records
- 7KE · 3-[3-(4-chlorophenyl)-1,2,4-oxadiazol-5-yl]propan-1-ol · in 2 records
- 7KJ · (7~{R})-7-[(3,5-dimethyl-1,2-oxazol-4-yl)methylamino]-3-[(4-methoxynaphthalen-1-yl)methyl]-5,6,7,8-tetrahydro-[1]benzothiolo[2,3-d]pyrimidin-4-one · in 2 records
- 8K9 · (1~{R},9~{S})-11-[(2~{R})-3-[2,4-bis(2-methylbutan-2-yl)phenoxy]-2-oxidanyl-propyl]-7,11-diazatricyclo[7.3.1.0^{2,7}]trideca-2,4-dien-6-one · in 2 records
- 8NO · 2-[[3-(2-phenylethoxy)phenyl]amino]benzamide · in 2 records
- A2I · 2-(4,6-dimethylpyrimidin-2-yl)sulfanyl-N-[3-(phenoxymethyl)phenyl]ethanamide · in 2 records
- A2X · 2-(4,6-dimethylpyrimidin-2-yl)sulfanyl-N-(4-phenylsulfanylphenyl)ethanamide · in 2 records
- KXG · [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-sulfanyl-oxolan-2-yl]methyl hydrogen phosphate · in 2 records
- KXJ · N~2~-[3-(2-hydroxyethoxy)propanoyl]-N-phenyl-N~6~-tetradecanethioyl-L-lysinamide · in 2 records
- L55 · N-[3-[[3-[2-(4,6-dimethylpyrimidin-2-yl) sulfanylethanoylamino]phenyl]methoxy]phenyl]-1-methyl-pyrazole-4-carboxamide · in 2 records
- L5C · N-[4-[[3-[2-(4,6-dimethylpyrimidin-2-yl) sulfanylethanoylamino]phenyl]methoxy]phenyl]-1-methyl-pyrazole-4-carboxamide · in 2 records
- NA · Sodium ion · in 2 records
- NCA · Nicotinamide · in 2 records
- OMR · [(2S,3R,4R,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2,4-bis(oxidanyl)oxolan-3-yl] tetradecanoate · in 2 records
- P6S · benzyl hydrogen carbonate · in 2 records
- QUE · 3,5,7,3',4'-pentahydroxyflavone · in 2 records
- WU3 · (2S)-2-dodecylsulfanylpropanoic acid · in 2 records
- WU8 · 3-dodecylsulfanyl-2,2-dimethyl-propanoic acid · in 2 records
- WWE · 3-dodecylsulfanyl-3-methyl-butanoic acid · in 2 records
- YDD · [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5S)-3,4-bis(oxidanyl)-5-tetradecoxy-oxolan-2-yl]methyl hydrogen phosphate · in 2 records
- YOY · [[(2S,3aS,5S,6R,6aS)-2-dodecyl-6-oxidanyl-3a,5,6,6a-tetrahydrofuro[2,3-d][1,3]dioxol-5-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate · in 2 records
- 5GN · N-{5-[(7-bromonaphthalen-1-yl)methyl]-1,3-thiazol-2-yl}-2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetamide · in 1 record
- 5GR · N-(5-{3-[(1-benzyl-1H-1,2,3-triazol-4-yl)methoxy]benzyl}-1,3-thiazol-2-yl)-2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetamide · in 1 record
- CL · Chloride ion · in 1 record
Experiment against prediction
- 6L72 chain A against the predicted model Q8IXJ6: TM-score 0.99, RMSD 0.82 Å
- 6L71 chain A against the predicted model Q8IXJ6: TM-score 0.98, RMSD 0.86 Å
- 6NR0 chain A against the predicted model Q8IXJ6: TM-score 0.98, RMSD 0.89 Å
- 4X3O chain A against the predicted model Q8IXJ6: TM-score 0.98, RMSD 0.90 Å
- 4X3O chain A against the predicted model Q8IXJ6: TM-score 0.98, RMSD 0.90 Å
- 8QTU chain A against the predicted model Q8IXJ6: TM-score 0.98, RMSD 0.92 Å
- 6L66 chain A against the predicted model Q8IXJ6: TM-score 0.98, RMSD 0.93 Å
- 8QT4 chain A against the predicted model Q8IXJ6: TM-score 0.98, RMSD 0.96 Å
- 8QT3 chain A against the predicted model Q8IXJ6: TM-score 0.98, RMSD 0.96 Å
- 8TGP chain A against the predicted model Q8IXJ6: TM-score 0.98, RMSD 0.93 Å
Elsewhere
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