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Structure paper

TitleDe-Novo Design of Cereblon (CRBN) Effectors Guided by Natural Hydrolysis Products of Thalidomide Derivatives.
Journal, issue, pagesJ. Med. Chem., Vol. 62, Page 6615-6629, Year 2019
Publish dateMar 13, 2019 (structure data deposition date)
AuthorsHeim, C. / Pliatsika, D. / Mousavizadeh, F. / Bar, K. / Hernandez Alvarez, B. / Giannis, A. / Hartmann, M.D.
External linksJ. Med. Chem. / PubMed:31251063
MethodsX-ray diffraction
Resolution1.1 - 1.94 Å
Structure data

PDB-6r0q:
Mutant cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with thalidomide metabolite alpha-(o-carboxybenzamido)glutarimide
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-6r0s:
Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 4a and hydrolysis product
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

PDB-6r0u:
Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 5a and hydrolysis product
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-6r0v:
Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with hydrolysis product of compound 4b
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-6r11:
Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 5b
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-6r12:
Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7b
Method: X-RAY DIFFRACTION / Resolution: 1.74 Å

PDB-6r13:
Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7f
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-6r18:
Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 11a
Method: X-RAY DIFFRACTION / Resolution: 1.35 Å

PDB-6r19:
Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 20a
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-6r1a:
Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 20b
Method: X-RAY DIFFRACTION / Resolution: 1.54 Å

PDB-6r1c:
Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 12a
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-6r1d:
Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7d, co-crystallized
Method: X-RAY DIFFRACTION / Resolution: 1.1 Å

PDB-6r1k:
Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7c
Method: X-RAY DIFFRACTION / Resolution: 1.94 Å

PDB-6r1w:
Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 16b
Method: X-RAY DIFFRACTION / Resolution: 1.35 Å

PDB-6r1x:
Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7a
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-JNW:
2-[[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamoyl]benzoic acid

ChemComp-HOH:
WATER

ChemComp-EF2:
S-Thalidomide / medication*YM

ChemComp-PO4:
PHOSPHATE ION

ChemComp-JOE:
2-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyl]-6-nitro-benzoic acid

ChemComp-CL:
Unknown entry

ChemComp-JOH:
2-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-4-nitro-isoindole-1,3-dione

ChemComp-JO8:
3-azanyl-2-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyl]benzoic acid

ChemComp-JO5:
4-azanyl-2-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]isoindole-1,3-dione

ChemComp-JO2:
2-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyl]-4-nitro-benzoic acid

ChemComp-JOB:
5-azanyl-2-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]isoindole-1,3-dione

ChemComp-JOT:
~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-2-phenyl-ethanamide

ChemComp-JOK:
~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-3-phenyl-propanamide

ChemComp-JOQ:
[4-(aminomethyl)phenyl]methyl ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamate

ChemComp-JON:
[(2~{S})-pyrrolidin-2-yl]methyl ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamate

ChemComp-JP8:
[(2~{R})-pyrrolidin-2-yl]methyl ~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamate

ChemComp-ASP:
ASPARTIC ACID

ChemComp-JOW:
4-[[4-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyloxymethyl]phenyl]methylamino]-4-oxidanylidene-butanoic acid

ChemComp-JP5:
(phenylmethyl) ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamate

ChemComp-JPB:
~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-2,4,6-tris(chloranyl)benzamide

ChemComp-JPW:
(4-azanylcyclohexyl)methyl ~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamate

ChemComp-JPQ:
~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-3-methyl-but-2-enamide

Source
  • magnetospirillum gryphiswaldense msr-1 (magnetotactic)
KeywordsSIGNALING PROTEIN / proteolysis targeting chimera / PROTAC / protein degradation / hydrolysis product / ----

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