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Structure paper

TitleStructure-Based Design of Inhibitors Selective for Human Proteasome beta 2c or beta 2i Subunits.
Journal, issue, pagesJ. Med. Chem., Vol. 62, Page 1626-1642, Year 2019
Publish dateOct 3, 2018 (structure data deposition date)
AuthorsXin, B.T. / Huber, E.M. / de Bruin, G. / Heinemeyer, W. / Maurits, E. / Espinal, C. / Du, Y. / Janssens, M. / Weyburne, E.S. / Kisselev, A.F. ...Xin, B.T. / Huber, E.M. / de Bruin, G. / Heinemeyer, W. / Maurits, E. / Espinal, C. / Du, Y. / Janssens, M. / Weyburne, E.S. / Kisselev, A.F. / Florea, B.I. / Driessen, C. / van der Marel, G.A. / Groll, M. / Overkleeft, H.S.
External linksJ. Med. Chem. / PubMed:30657666
MethodsX-ray diffraction
Resolution2.3 - 3.4 Å
Structure data

PDB-6htb:
Yeast 20S proteasome with human beta2c (S171G)
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-6htc:
Yeast 20S proteasome with human beta2c (S171G) in complex with ONX 0914
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-6htd:
Yeast 20S proteasome with human beta2c (S171G) in complex with 4
Method: X-RAY DIFFRACTION / Resolution: 3.0 Å

PDB-6htp:
Yeast 20S proteasome with human beta2c (S171G) in complex with 7
Method: X-RAY DIFFRACTION / Resolution: 3.0 Å

PDB-6htr:
Yeast 20S proteasome with human beta2c (S171G) in complex with 13
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-6hub:
Yeast 20S proteasome with human beta2c (S171G) in complex with 16
Method: X-RAY DIFFRACTION / Resolution: 2.9 Å

PDB-6huc:
Yeast 20S proteasome with human beta2c (S171G) in complex with 18
Method: X-RAY DIFFRACTION / Resolution: 3.0 Å

PDB-6huq:
Yeast 20S proteasome with human beta2c (S171G) in complex with 20
Method: X-RAY DIFFRACTION / Resolution: 3.0 Å

PDB-6huu:
Yeast 20S proteasome with human beta2c (S171G) in complex with 29
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-6huv:
Yeast 20S proteasome with human beta2c (S171G) in complex with 39
Method: X-RAY DIFFRACTION / Resolution: 3.1 Å

PDB-6hv3:
Yeast 20S proteasome with human beta2i (1-53)
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-6hv4:
Yeast 20S proteasome with human beta2i (1-53) in complex with ONX 0914
Method: X-RAY DIFFRACTION / Resolution: 3.0 Å

PDB-6hv5:
Yeast 20S proteasome with human beta2i (1-53) in complex with 4
Method: X-RAY DIFFRACTION / Resolution: 3.0 Å

PDB-6hv7:
Yeast 20S proteasome with human beta2i (1-53) in complex with 7
Method: X-RAY DIFFRACTION / Resolution: 3.4 Å

PDB-6hva:
Yeast 20S proteasome with human beta2i (1-53) in complex with 13
Method: X-RAY DIFFRACTION / Resolution: 2.9 Å

PDB-6hvr:
Yeast 20S proteasome with human beta2i (1-53) in complex with 16
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-6hvs:
Yeast 20S proteasome with human beta2i (1-53) in complex with 18
Method: X-RAY DIFFRACTION / Resolution: 3.1 Å

PDB-6hvt:
Yeast 20S proteasome with human beta2i (1-53) in complex with 20
Method: X-RAY DIFFRACTION / Resolution: 2.9 Å

PDB-6hvu:
Yeast 20S proteasome with human beta2i (1-53) in complex with 29
Method: X-RAY DIFFRACTION / Resolution: 2.9 Å

PDB-6hvv:
Yeast 20S proteasome with human beta2i (1-53) in complex with 39
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-6hvw:
Yeast 20S proteasome with human beta2i (1-53) in complex with 43
Method: X-RAY DIFFRACTION / Resolution: 3.0 Å

PDB-6hvx:
Yeast 20S proteasome in complex with 4
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-6hvy:
Yeast 20S proteasome in complex with 5 (7- and 6-membered ring)
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-6hw0:
Yeast 20S proteasome in complex with 7
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-6hw3:
Yeast 20S proteasome in complex with 13
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-6hw4:
Yeast 20S proteasome in complex with 16
Method: X-RAY DIFFRACTION / Resolution: 2.9 Å

PDB-6hw5:
Yeast 20S proteasome in complex with 18
Method: X-RAY DIFFRACTION / Resolution: 2.9 Å

PDB-6hw6:
Yeast 20S proteasome in complex with 20
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-6hw7:
Yeast 20S proteasome in complex with 29
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-6hw8:
Yeast 20S proteasome in complex with 39
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-6hw9:
Yeast 20S proteasome in complex with 41b
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-6hwa:
Yeast 20S proteasome in complex with 43
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-6hwb:
Yeast 20S proteasome in complex with 44b
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-6hwc:
Yeast 20S proteasome beta2-G45A mutant
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-6hwd:
Yeast 20S proteasome beta2-G45A mutant in complex with bortezomib
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-6hwe:
Yeast 20S proteasome beta2-G45A mutant in complex with carfilzomib
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-6hwf:
Yeast 20S proteasome beta2-G45A mutant in complex with ONX 0914
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-CL:
Unknown entry / Chloride

ChemComp-HOH:
WATER / Water

ChemComp-GQK:
(2~{S})-3-(4-methoxyphenyl)-~{N}-[(2~{S},3~{R})-4-methyl-3,4-bis(oxidanyl)-1-phenyl-pentan-2-yl]-2-[[(2~{S})-2-(2-morpholin-4-ylethanoylamino)propanoyl]amino]propanamide

ChemComp-MES:
2-(N-MORPHOLINO)-ETHANESULFONIC ACID / pH buffer*YM / MES (buffer)

ChemComp-SO4:
SULFATE ION / Sulfate

ChemComp-GQH:
(2~{S})-~{N}-[(2~{S})-1-[[(2~{S})-1-[4-(aminomethyl)phenyl]-4-methylsulfonyl-butan-2-yl]amino]-1-oxidanylidene-propan-2-yl]-2-[[(2~{S})-2-azido-3-phenyl-propanoyl]amino]-4-methyl-pentanamide

ChemComp-GQQ:
~{N}-[(2~{S})-1-[[(2~{S})-1-[[(2~{S})-1-[4-(aminomethyl)phenyl]-4-methylsulfonyl-butan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]pyrazine-2-carboxamide

ChemComp-GQT:
(2~{S})-~{N}-[(2~{S})-1-[[(2~{S})-1-[4-(aminomethyl)phenyl]-4-methylsulfonyl-butan-2-yl]amino]-3-oxidanyl-1-oxidanylidene-propan-2-yl]-2-[[(2~{S})-2-azido-3-phenyl-propanoyl]amino]-4-methyl-pentanamide

ChemComp-GRW:
(2~{S})-~{N}-[(2~{S},3~{R})-1-[[(2~{S})-1-[4-(aminomethyl)phenyl]-4-methylsulfonyl-butan-2-yl]amino]-3-oxidanyl-1-oxidanylidene-butan-2-yl]-2-[[(2~{R})-2-azido-3-phenyl-propanoyl]amino]-4-methyl-pentanamide

ChemComp-GRT:
(2~{S})-~{N}-[2-[[(2~{S})-1-[4-(aminomethyl)phenyl]-4-methylsulfonyl-butan-2-yl]amino]-2-oxidanylidene-ethyl]-2-[[(2~{S})-2-azido-3-phenyl-propanoyl]amino]-4-methyl-pentanamide

ChemComp-GT5:
~{N}-[(2~{S})-1-[[(2~{S})-1-[[(2~{S})-1-[4-(aminomethyl)phenyl]-4-methylsulfonyl-butan-2-yl]amino]-3-methoxy-1-oxidanylidene-propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-2-methyl-1,3-thiazole-5-carboxamide

ChemComp-GTW:
~{N}-[(2~{S})-1-[[(2~{S})-1-[[(2~{S})-1-[4-(aminomethyl)phenyl]-4-methylsulfonyl-butan-2-yl]amino]-3-cyclohexyl-1-oxidanylidene-propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-2-methyl-1,3-thiazole-5-carboxamide

ChemComp-GT8:
(2~{S})-~{N}-[(3~{S},4~{R})-1-cyclohexyl-5-methyl-4,5-bis(oxidanyl)hexan-3-yl]-3-(4-methoxyphenyl)-2-[[(2~{S})-2-(2-morpholin-4-ylethanoylamino)propanoyl]amino]propanamide

ChemComp-GVW:
(2~{S})-~{N}-[(2~{S},3~{R})-1-[(4~{a}~{S},8~{a}~{S})-1,2,3,4,4~{a},5,6,7,8,8~{a}-decahydronaphthalen-2-yl]-4-methyl-3,4-bis(oxidanyl)pentan-2-yl]-3-(4-methoxyphenyl)-2-[[(2~{S})-2-(2-morpholin-4-ylethanoylamino)propanoyl]amino]propanamide

ChemComp-GVZ:
(2~{S})-~{N}-[(2~{S},3~{R})-1-[(1~{S},4~{a}~{S},8~{a}~{R})-1,2,3,4,4~{a},5,6,7,8,8~{a}-decahydronaphthalen-1-yl]-4-methyl-3,4-bis(oxidanyl)pentan-2-yl]-3-(4-methoxyphenyl)-2-[[(2~{S})-2-(2-morpholin-4-ylethanoylamino)propanoyl]amino]propanamide

ChemComp-GW2:
(2~{S})-~{N}-[(2~{S},3~{S},4~{R})-1-[(1~{S},4~{a}~{S},8~{a}~{R})-1,2,3,4,4~{a},5,6,7,8,8~{a}-decahydronaphthalen-1-yl]-4-methyl-3,5-bis(oxidanyl)pentan-2-yl]-3-(4-methoxyphenyl)-2-[[(2~{S})-2-(2-morpholin-4-ylethanoylamino)propanoyl]amino]propanamide

ChemComp-GWK:
(2~{S})-3-(4-methoxyphenyl)-~{N}-[(2~{S},3~{R})-4-methyl-1-(4-methylcyclohexyl)-3,4-bis(oxidanyl)pentan-2-yl]-2-[[(2~{S})-2-(2-morpholin-4-ylethanoylamino)propanoyl]amino]propanamide

ChemComp-GWT:
(2~{S})-~{N}-[(2~{S},3~{R})-1-(4-cyclohexylcyclohexyl)-4-methyl-3,4-bis(oxidanyl)pentan-2-yl]-3-(4-methoxyphenyl)-2-[[(2~{S})-2-(2-morpholin-4-ium-4-ylethanoylamino)propanoyl]amino]propanamide

ChemComp-BO2:
N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE / medication, anticancer*YM / Bortezomib

ChemComp-GWZ:
(2~{S})-~{N}-[(2~{S})-1-[[(3~{R},4~{S})-2,6-dimethyl-2,3-bis(oxidanyl)heptan-4-yl]amino]-1-oxidanylidene-3-phenyl-propan-2-yl]-4-methyl-2-[[(2~{S})-2-(2-morpholin-4-ylethanoylamino)-4-phenyl-butanoyl]amino]pentanamide

Source
  • homo sapiens (human)
  • saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast)
  • saccharomyces cerevisiae s288c (yeast)
KeywordsHYDROLASE / Proteasome / Mutant / Inhibitor / Binding Analysis

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