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TitlePaying the Price of Desolvation in Solvent-Exposed Protein Pockets: Impact of Distal Solubilizing Groups on Affinity and Binding Thermodynamics in a Series of Thermolysin Inhibitors.
Journal, issue, pagesJ. Med. Chem., Vol. 60, Page 5791-5799, Year 2017
Publish dateDec 13, 2016 (structure data deposition date)
AuthorsCramer, J. / Krimmer, S.G. / Heine, A. / Klebe, G.
External linksJ. Med. Chem. / PubMed:28590130
MethodsX-ray diffraction
Resolution1.12 - 1.379 Å
Structure data

PDB-5mnr:
Thermolysin in complex with inhibitor JC256
Method: X-RAY DIFFRACTION / Resolution: 1.249 Å

PDB-5n2t:
Thermolysin in complex with inhibitor JC287
Method: X-RAY DIFFRACTION / Resolution: 1.379 Å

PDB-5n2x:
Thermolysin in complex with inhibitor JC272
Method: X-RAY DIFFRACTION / Resolution: 1.209 Å

PDB-5n2z:
Thermolysin in complex with inhibitor JC286
Method: X-RAY DIFFRACTION / Resolution: 1.37 Å

PDB-5n31:
Thermolysin in complex with inhibitor JC277
Method: X-RAY DIFFRACTION / Resolution: 1.368 Å

PDB-5n34:
Thermolysin in complex with inhibitor JC276
Method: X-RAY DIFFRACTION / Resolution: 1.22 Å

PDB-5n3v:
Thermolysin in complex with inhibitor JC292
Method: X-RAY DIFFRACTION / Resolution: 1.12 Å

PDB-5n3y:
Thermolysin in complex with inhibitor JC267
Method: X-RAY DIFFRACTION / Resolution: 1.339 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-CA:
Unknown entry

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

ChemComp-JC2:
(2~{S})-4-azanyl-2-[[(2~{S})-4-methyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]pentanoyl]amino]butanoic acid

ChemComp-MPD:
(4S)-2-METHYL-2,4-PENTANEDIOL / precipitant*YM

ChemComp-HOH:
WATER

ChemComp-8KK:
~{N}-[(2~{S})-1-(3-azanylpropylamino)-4-methyl-1-oxidanylidene-pentan-2-yl]-(phenylmethoxycarbonylaminomethyl)phosphonamidic acid

ChemComp-8KN:
(2~{S})-5-azanyl-2-[[(2~{S})-4-methyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]pentanoyl]amino]pentanoic acid

ChemComp-8JH:
~{N}-[(2~{S})-1-(4-azanylbutylamino)-4-methyl-1-oxidanylidene-pentan-2-yl]-(phenylmethoxycarbonylaminomethyl)phosphonamidic acid

ChemComp-8LB:
(2~{S})-6-azanyl-2-[[(2~{S})-4-methyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]pentanoyl]amino]hexanoic acid

ChemComp-8JQ:
~{N}-[(2~{S})-1-(2-azanylethylamino)-4-methyl-1-oxidanylidene-pentan-2-yl]-(phenylmethoxycarbonylaminomethyl)phosphonamidic acid

ChemComp-8L5:
~{N}-[(2~{S})-1-(aminomethylamino)-4-methyl-1-oxidanylidene-pentan-2-yl]-(phenylmethoxycarbonylaminomethyl)phosphonamidic acid;hydrogen

ChemComp-8L2:
(2~{S})-3-azanyl-2-[[(2~{S})-4-methyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]pentanoyl]amino]propanoic acid

Source
  • bacillus thermoproteolyticus (bacteria)
KeywordsHYDROLASE / Inhibitor / Phosphonamidate / Protease

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