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Structure paper

TitleFragment-Based Discovery of a Novel, Brain Penetrant, Orally Active HDAC2 Inhibitor.
Journal, issue, pagesAcs Med. Chem. Lett., Vol. 13, Page 1591-1597, Year 2022
Publish dateMay 25, 2022 (structure data deposition date)
AuthorsTamanini, E. / Miyamura, S. / Buck, I.M. / Cons, B.D. / Dawson, L. / East, C. / Futamura, T. / Goto, S. / Griffiths-Jones, C. / Hashimoto, T. ...Tamanini, E. / Miyamura, S. / Buck, I.M. / Cons, B.D. / Dawson, L. / East, C. / Futamura, T. / Goto, S. / Griffiths-Jones, C. / Hashimoto, T. / Heightman, T.D. / Ishikawa, S. / Ito, H. / Kaneko, Y. / Kawato, T. / Kondo, K. / Kurihara, N. / McCarthy, J.M. / Mori, Y. / Nagase, T. / Nakaishi, Y. / Reeks, J. / Sato, A. / Schopf, P. / Tai, K. / Tamai, T. / Tisi, D. / Woolford, A.J.
External linksAcs Med. Chem. Lett. / PubMed:36262388
MethodsX-ray diffraction
Resolution1.52 - 2.168 Å
Structure data

PDB-7zzo:
HDAC2 in complex with an inhibitor
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-7zzp:
Structure of HDAC2 complexed with an inhibitory ligand
Method: X-RAY DIFFRACTION / Resolution: 1.52 Å

PDB-7zzr:
HDAC2 in complex with inhibitory ligand
Method: X-RAY DIFFRACTION / Resolution: 2.168 Å

PDB-7zzs:
HDAC2 complexed with an inhibitory ligand
Method: X-RAY DIFFRACTION / Resolution: 1.88 Å

PDB-7zzt:
Ligand binding to HDAC2
Method: X-RAY DIFFRACTION / Resolution: 1.56 Å

PDB-7zzu:
Inhibitory Ligand binding to HDAC2
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-7zzw:
Ligand binding to HDAC2
Method: X-RAY DIFFRACTION / Resolution: 1.73 Å

PDB-8a0b:
Inhibitor binding to HDAC2
Method: X-RAY DIFFRACTION / Resolution: 1.746 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-CA:
Unknown entry

ChemComp-NA:
Unknown entry

ChemComp-KIZ:
[(2~{R})-1-(dimethylamino)-3-(4-fluorophenyl)-1-oxidanylidene-propan-2-yl]azanium

ChemComp-PG4:
TETRAETHYLENE GLYCOL / precipitant*YM

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER

ChemComp-KZF:
2-(cyclohexylazaniumyl)ethanesulfonate / pH buffer*YM

ChemComp-HOH:
WATER

ChemComp-PGE:
TRIETHYLENE GLYCOL

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-KJ6:
6-methyl-4-oxidanyl-pyran-2-one

ChemComp-2OP:
(2S)-2-HYDROXYPROPANOIC ACID

ChemComp-NHE:
2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / pH buffer*YM

ChemComp-DMS:
DIMETHYL SULFOXIDE / DMSO, precipitant*YM

ChemComp-KJN:
[(2~{R})-1-(dimethylamino)-1-oxidanylidene-4-phenyl-butan-2-yl]azanium

ChemComp-SHH:
OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE

ChemComp-KK0:
(5~{S})-5-(4-chlorophenyl)pyrrolidin-2-one

ChemComp-KJF:
[(2~{R})-1-oxidanylidene-4-phenyl-1-pyrrolidin-1-yl-butan-2-yl]azanium

ChemComp-KKI:
2-[4-[(2~{R},4~{S})-4-phenylpyrrolidin-2-yl]carbonylpiperazin-1-yl]pyridine-3-carbonitrile

ChemComp-KKW:
[(2~{R},4~{S})-4-(3-chlorophenyl)pyrrolidin-2-yl]-(4-thieno[2,3-c]pyridin-7-ylpiperazin-1-yl)methanone

ChemComp-KRU:
1,3-dihydroisoindol-2-yl-[(2R,4S)-4-phenylpyrrolidin-1-ium-2-yl]methanone

Source
  • homo sapiens (human)
KeywordsTRANSCRIPTION / histone deacetylase / chromatin binding / protein complex / transcription regulation / Deacetylase / transcription regulator / protein de-acetylation / deactylase activity / cell cycle progression / protein deacetylation / transcriptional repressor complex

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