UniProt Q92769
Histone deacetylase 2 (Q92769)
Histone deacetylase 2 (UniProt Q92769), EC 3.5.1.-, 3.5.1.98: 41 experimental structures and 1 predicted model on GenesisL1, 27 ligands bound, 29 pockets. Binding sites, druggability and experiment against prediction (TM-score)…
- UniProt
- Q92769
- Protein
- Histone deacetylase 2
- EC
- 3.5.1.-, 3.5.1.98
- Experimental structures
- 41
- Predicted models
- 1
- Ligands
- 27
- Pockets
- 29 · 5 records with a druggable one
Structures
42 records of Q92769 in the MolNFT archive: 41 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 3MAX | Crystal Structure of Human HDAC2 complexed with an N-(2-aminophenyl)benzamide | x-ray diffraction | A, B, C | — | — |
| 3MAX | Crystal structure of human HDAC2 complexed with an N-(2-aminophenyl) benzamide | x-ray diffraction | A, B, C | — | — |
| 4LXZ | Structure of Human HDAC2 in complex with SAHA (vorinostat) | x-ray diffraction | A, B, C | — | — |
| 4LXZ | Structure of human HDAC2 in complex with saha (vorinostat) | x-ray diffraction | A, B, C | — | — |
| 4LY1 | Structure of Human HDAC2 in complex with inhibitor 4-(acetylamino)-N-[2-amino-5-(thiophen-2-yl)pheny… | x-ray diffraction | A, B, C | — | — |
| 4LY1 | Structure of human HDAC2 in complex with inhibitor 4-(acetylamino)-N… | x-ray diffraction | A, B, C | — | — |
| 5IWG | HDAC2 with ligand BRD4884 | x-ray diffraction | A, B, C | ZN, CA, IWX | — |
| 5IWG | HDAC2 with ligand BRD4884 | x-ray diffraction | A, B, C | — | — |
| 5IX0 | HDAC2 with ligand BRD7232 | x-ray diffraction | A, B, C | ZN, CA, 6EZ | 5 (best 0.74) |
| 5IX0 | HDAC2 with ligand BRD7232 | x-ray diffraction | A, B, C | — | — |
| 6G3O | Crystal structure of human HDAC2 in complex with (R)-6-[3,4-Dioxo-2-(4-trifluoromethoxy-phenylamino)… | x-ray diffraction | A, B, C | ZN, CA, NA, EL8, SO4 | — |
| 6G3O | Crystal structure of human HDAC2 in complex with (R)-6-[3,4-dioxo-2… | x-ray diffraction | A, B, C | ZN, CA, NA, EL8, SO4 | — |
| 6WBW | Structure of human HDAC2 in complex with an ethyl ketone inhibitor | x-ray diffraction | A, B, C | TV1, ZN, CA | — |
| 6WBZ | Structure of human HDAC2 in complex with an ethyl ketone inhibitor containing a spiro-bicyclic group | x-ray diffraction | A, B, C | ZN, SO4, CA, TV7 | — |
| 6WHN | Histone deacetylases complex with peptide macrocycles | x-ray diffraction | A, B, C | ZN, NA | — |
| 6WHO | Histone deacetylases complex with peptide macrocycles | x-ray diffraction | A, B, C | ZN, NA | — |
| 6WHQ | Histone deacetylases complex with peptide macrocycles | x-ray diffraction | A, B, C | ZN, NA | — |
| 6WHZ | Histone deacetylases complex with peptide macrocycles | x-ray diffraction | A, B, C | ZN, NA | — |
| 6WI3 | Histone deacetylases complex with peptide macrocycles | x-ray diffraction | A, B, C | ZN, NA | — |
| 6XDM | Structure of human HDAC2 in complex with an aryl ketone inhibitor | x-ray diffraction | A, B, C | ZN, CA, SO4, V1D | — |
| 6XDM | Structure of human HDAC2 in complex with an aryl ketone inhibitor | x-ray diffraction | A, B, C | ZN, CA, SO4, V1D | — |
| 6XEB | Structure of human HDAC2 in complex with ketone inhibitor (compound E) | x-ray diffraction | A, B, C | ZN, SO4, CA, V1P | — |
| 6XEB | Structure of human HDAC2 in complex with ketone inhibitor (compound E) | x-ray diffraction | A, B, C | ZN, SO4, CA, V1P | — |
| 6XEC | Structure of human HDAC2 in complex with ketone inhibitor (compound O) | x-ray diffraction | A, B, C | ZN, SO4, CA, V1S | — |
| 7JS8 | Structure of human HDAC2 in complex with an ethyl ketone inhibitor containing a spiro-bicyclic… | x-ray diffraction | A, B, C | ZN, SO4, CA, VJV | — |
| 7KBG | Structure of Human HDAC2 in complex with a 2-substituted benzamide inhibitor (compound 20) | x-ray diffraction | A, B, C | ZN, CA, SO4, WBA, WBD | — |
| 7KBG | Structure of human HDAC2 in complex with a 2-substituted benzamide inhibitor (compound 20) | x-ray diffraction | A, B, C | ZN, CA, SO4, WBA, WBD | — |
| 7KBH | Structure of human HDAC2 in complex with a 2-substituted benzamide inhibitor (compound 16) | x-ray diffraction | A, B, C | ZN, CA, WB4 | — |
| 7LTG | Structure of human HDAC2 in complex with apicidin | x-ray diffraction | A, B, C | ZN, CA, YED | 4 (best 0.73) |
| 7LTG | Structure of human HDAC2 in complex with apicidin | x-ray diffraction | A, B, C | ZN, CA, YED | — |
| 7LTK | Structure of human HDAC2 in complex with an inhibitor that lacks a zinc binding group (compound 12) | x-ray diffraction | A, B, C | ZN, CA, YEM | — |
| 7LTL | Structure of human HDAC2 in complex with an inhibitor lacking a zinc binding group (compound 19) | x-ray diffraction | A, B, C | ZN, SO4, CA, YEV | — |
| 7MOS | Structure of HDAC2 in complex with a macrocyclic inhibitor (compound 4) | x-ray diffraction | A, B, C | ZN, SO4, CA, ZLV | — |
| 7MOT | Structure of HDAC2 in complex with an inhibitor (compound 9) | x-ray diffraction | A, B, C | ZN, SO4, CA, V1P | — |
| 7MOX | Structure of HDAC2 in complex with an inhibitor (compound 14) | x-ray diffraction | A, B, C | ZN, SO4, CA, ZLS | — |
| 7MOX | Structure of HDAC2 in complex with an inhibitor (compound 14) | x-ray diffraction | A, B, C | ZN, SO4, CA, ZLS | — |
| 7MOY | Structure of HDAC2 in complex with an inhibitor (compound 19) | x-ray diffraction | A, B, C | ZN, SO4, CA, ZLM | 4 (best 0.73) |
| 7MOY | Structure of HDAC2 in complex with an inhibitor (compound 19) | x-ray diffraction | A, B, C | ZN, SO4, CA, ZLM | — |
| 7MOZ | Structure of HDAC2 in complex with a macrocyclic inhibitor (compound 25) | x-ray diffraction | A, B, C | ZN, SO4, CA, ZL4 | — |
| 7ZZS | HDAC2 complexed with an inhibitory ligand | x-ray diffraction | A, B, C | ZN, CA, NA, SHH, KK0, KZF | 8 (best 0.71) |
| 8A0B | Inhibitor binding to HDAC2 | x-ray diffraction | A, B, C | ZN, CA, NA, KRU | 8 (best 0.72) |
| Q92769 | AlphaFold monomer V2.0 prediction for histone deacetylase 2 (Q92769) | predicted | A | — | — |
Ligands
- ZN · Zinc ion · in 33 records
- CA · Calcium ion · in 28 records
- SO4 · Sulfate ion · in 19 records
- NA · Sodium ion · in 9 records
- V1P · 5-{(1S)-7,7-dihydroxy-1-[(1-methylazetidine-3-carbonyl)amino]nonyl}-2-phenyl-1H-imidazole-4-carboxamide · in 3 records
- EL8 · (6~{R})-6-[[3,4-bis(oxidanylidene)-2-[[4-(trifluoromethyloxy)phenyl]amino]cyclobuten-1-yl]amino]-~{N}-oxidanyl-heptanamide · in 2 records
- V1D · N-[(1S)-1-[4-(2-fluorophenyl)-1H-imidazol-2-yl]-7,7-dihydroxy-7-(1,2-oxazol-3-yl)heptyl]-1-methylazetidine-3-carboxamide · in 2 records
- WBA · N-{(1S)-5-[(2-fluoro-6-hydroxybenzene-1-carbonyl) amino]-1-[5-(naphthalen-2-yl)-1H-imidazol-2-yl]pentyl}-1,3-thiazole-5-carboxamide · in 2 records
- WBD · 2,5-dichloro-1H-benzimidazole · in 2 records
- YED · (3s,6s,9s,15ar)-9-[(2S)-butan-2-yl]-3-(6,6-dihydroxyoctyl)-6-[(1-methoxy-1H-indol-3-yl) methyl]octahydro-2H-pyrido[1,2-A][1,4,7, 10]tetraazacyclododecine-1,4,7,10(3H,12H)-tetrone · in 2 records
- ZLM · (1S)-6-ethyl-N-{(1S)-1-[5-(2-ethyl-1-oxo-1,2-dihydroisoquinolin-6-yl)-1H-imidazol-2-yl]-7,7-dihydroxynonyl}-6-azaspiro[2.5]octane-1-carboxamide · in 2 records
- ZLS · (1S)-N-[(1S)-7,7-dihydroxy-1-{4-[(1R,4S)-1,2,3,4-tetrahydro-1,4-methanonaphthalen-6-yl]-1H-imidazol-2-yl}nonyl]-6-methyl-6-azaspiro[2.5]octane-1-carboxamide · in 2 records
- 6EZ · (3-exo)-N-(4-amino-4'-fluoro[1,1'-biphenyl]-3-yl)-8-oxabicyclo[3.2.1]octane-3-carboxamide · in 1 record
- IWX · N-(4-amino-4'-fluoro[1,1'-biphenyl]-3-yl)oxane-4-carboxamide · in 1 record
- KK0 · (5~{S})-5-(4-chlorophenyl)pyrrolidin-2-one · in 1 record
- KRU · 1,3-dihydroisoindol-2-yl-[(2R,4S)-4-phenylpyrrolidin-1-ium-2-yl]methanone · in 1 record
- KZF · 2-(cyclohexylazaniumyl)ethanesulfonate · in 1 record
- SHH · Octanedioic acid hydroxyamide phenylamide · in 1 record
- TV1 · N-{(1S)-7,7-dihydroxy-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]nonyl}-1-methylazetidine-3-carboxamide · in 1 record
- TV7 · (1S)-N-{(1S)-7,7-dihydroxy-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]nonyl}-6-ethyl-6-azaspiro[2.5]octane-1-carboxamide · in 1 record
- V1S · (1S)-N-{(1S)-1-[5-cyano-2-(4-fluorophenyl)-1H-imidazol-4-yl]-7,7-dihydroxynonyl}-6-methyl-6-azaspiro[2.5]octane-1-carboxamide · in 1 record
- VJV · (1S)-N-{(1S)-7,7-dihydroxy-1-[4-(2-methylquinolin-6-yl)-1H-imidazol-2-yl]nonyl}-6-methyl-6-azaspiro[2.5]octane-1-carboxamide · in 1 record
- WB4 · N-{(1S)-5-{[2-(methylsulfanyl)benzene-1-carbonyl]amino}-1-[5-(naphthalen-2-yl)-1H-imidazol-2-yl]pentyl}-1,3-thiazole-5-carboxamide · in 1 record
- YEM · N-{(1S)-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]pentyl}-1-methylazetidine-3-carboxamide · in 1 record
- YEV · (2R)-2-(5-hydroxy-2-methyl-1H-indol-3-yl)-N-{(1S)-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]pentyl}propanamide · in 1 record
- ZL4 · (1R,3S,6S,18R,27R)-6-(6,6-dihydroxyoctyl)-5,8,18,27,34-pentaazahexacyclo[25.2.2.1~7,10~.1~11,15~.1~14, 18~.0~1,3~]tetratriaconta-7,9,11(33),12,14,16-hexaene-4,32-dione (non-preferred name) · in 1 record
- ZLV · (3s,18s,20ar)-18-(6,6-dihydroxyoctyl)-1,5,6,7,8,18,19, 20A-octahydro-4H-14,17-epiminoazeto[1,2-G][1,7,10, 13]benzoxatriazacycloheptadecin-20(2H)-one · in 1 record
Experiment against prediction
- 7LTK chain B against the predicted model Q92769: TM-score 1.00, RMSD 0.23 Å
- 7LTL chain B against the predicted model Q92769: TM-score 1.00, RMSD 0.23 Å
- 7LTG chain B against the predicted model Q92769: TM-score 1.00, RMSD 0.25 Å
- 7LTG chain B against the predicted model Q92769: TM-score 1.00, RMSD 0.25 Å
- 6WHO chain B against the predicted model Q92769: TM-score 1.00, RMSD 0.25 Å
- 6WBW chain B against the predicted model Q92769: TM-score 1.00, RMSD 0.25 Å
- 7MOS chain B against the predicted model Q92769: TM-score 1.00, RMSD 0.25 Å
- 6WI3 chain B against the predicted model Q92769: TM-score 1.00, RMSD 0.26 Å
- 7KBG chain B against the predicted model Q92769: TM-score 1.00, RMSD 0.26 Å
- 7KBG chain B against the predicted model Q92769: TM-score 1.00, RMSD 0.26 Å
Elsewhere
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