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Structure paper

TitleSystematic Potency and Property Assessment of VHL Ligands and Implications on PROTAC Design.
Journal, issue, pagesChemmedchem, Vol. 18, Page e202200615-e202200615, Year 2023
Publish dateOct 19, 2022 (structure data deposition date)
AuthorsKrieger, J. / Sorrell, F.J. / Wegener, A.A. / Leuthner, B. / Machrouhi-Porcher, F. / Hecht, M. / Leibrock, E.M. / Muller, J.E. / Eisert, J. / Hartung, I.V. / Schlesiger, S.
External linksChemmedchem / PubMed:36749883
MethodsX-ray diffraction
Resolution1.72 - 3.18 Å
Structure data

PDB-8bdi:
VCB in complex with compound 32
Method: X-RAY DIFFRACTION / Resolution: 2.108 Å

PDB-8bdj:
VCB in complex with compound 30
Method: X-RAY DIFFRACTION / Resolution: 2.02 Å

PDB-8bdl:
VCB in complex with compound 27
Method: X-RAY DIFFRACTION / Resolution: 2.295 Å

PDB-8bdm:
VCB in complex with compound 26
Method: X-RAY DIFFRACTION / Resolution: 2.021 Å

PDB-8bdn:
VCB in complex with compound 23
Method: X-RAY DIFFRACTION / Resolution: 2.76 Å

PDB-8bdo:
VCB in complex with compound 21
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-8bds:
Ternary complex between VCB, BRD4-BD1 and PROTAC 48
Method: X-RAY DIFFRACTION / Resolution: 1.72 Å

PDB-8bdt:
Ternary complex between VCB, BRD4-BD2 and PROTAC 51
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-8bdx:
Ternary complex between VCB, BRD4-BD2 and PROTAC 48
Method: X-RAY DIFFRACTION / Resolution: 2.93 Å

PDB-8beb:
Ternary complex between VCB, BRD4-BD1 and PROTAC 49
Method: X-RAY DIFFRACTION / Resolution: 3.18 Å

Chemicals

ChemComp-QF7:
(2~{S},4~{R})-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[(1~{S})-3-(methylamino)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-3-oxidanylidene-propyl]-4-oxidanyl-pyrrolidine-2-carboxamide

ChemComp-HOH:
WATER

ChemComp-QE0:
(2~{S},4~{R})-~{N}-[(1~{S})-1-[4-chloranyl-2-(2-methoxyethoxy)phenyl]ethyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide

ChemComp-QF3:
(2~{S},4~{R})-~{N}-[(1~{S})-1-[2-(2-methoxyethoxy)-4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide

ChemComp-QE9:
(2~{S},4~{R})-~{N}-[[2-(2-methoxyethoxy)-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide

ChemComp-QFR:
(2~{R})-3-methyl-1-[(2~{S},4~{R})-2-[(5~{R})-5-methyl-5-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-4~{H}-1,2,4-oxadiazol-3-yl]-4-oxidanyl-pyrrolidin-1-yl]-2-(3-methyl-1,2-oxazol-5-yl)butan-1-one

ChemComp-QFF:
(2~{S},4~{R})-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-~{N}-[4-(4-methyl-1,3-thiazol-5-yl)phenoxy]-4-oxidanyl-pyrrolidine-2-carboxamide

ChemComp-SO4:
SULFATE ION

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-QIY:
(2S,4R)-N-[(1S)-1-(4-chlorophenyl)-3-[2-[2-[2-[2-[2-[(9S)-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8$l^{5},11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethylamino]-3-oxidanylidene-propyl]-1-[(2R)-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide

ChemComp-QLX:
(2~{S},4~{R})-~{N}-[(1~{S})-3-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethylamino]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-3-oxidanylidene-propyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide

ChemComp-MLI:
MALONATE ION

ChemComp-QIK:
(2~{S},4~{R})-~{N}-[(1~{S})-3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]butylamino]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-3-oxidanylidene-propyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide

Source
  • homo sapiens (human)
KeywordsLIGASE / PROTAC / degrader / complex / E3 ligase / VHL / VCB / VH032 / Ternary complex

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