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Structure paper

TitleExperimental and computational active site mapping as a starting point to fragment-based lead discovery.
Journal, issue, pagesChemmedchem, Vol. 7, Page 248-261, Year 2012
Publish dateApr 29, 2010 (structure data deposition date)
AuthorsBehnen, J. / Koster, H. / Neudert, G. / Craan, T. / Heine, A. / Klebe, G.
External linksChemmedchem / PubMed:22213702
MethodsX-ray diffraction
Resolution1.22 - 2.09 Å
Structure data

PDB-3ms3:
Crystal structure of Thermolysin in complex with Aniline
Method: X-RAY DIFFRACTION / Resolution: 1.54 Å

PDB-3msa:
Crystal structure of Thermolysin in complex with 3-Bromophenol
Method: X-RAY DIFFRACTION / Resolution: 1.66 Å

PDB-3msf:
Crystal structure of Thermolysin in complex with Urea
Method: X-RAY DIFFRACTION / Resolution: 2.09 Å

PDB-3msn:
Crystal structure of Thermolysin in complex with N-methylurea
Method: X-RAY DIFFRACTION / Resolution: 1.97 Å

PDB-3n21:
Crystal structure of Thermolysin in complex with S-1,2-Propandiol
Method: X-RAY DIFFRACTION / Resolution: 1.87 Å

PDB-3n4a:
Crystal structure of D-Xylose Isomerase in complex with S-1,2-Propandiol
Method: X-RAY DIFFRACTION / Resolution: 1.94 Å

PDB-3n9w:
Crystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) in complex with 1,2-Propanediol
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-3nn7:
Crystal structure of Thermolysin in complex with 2-bromoacetate
Method: X-RAY DIFFRACTION / Resolution: 2.05 Å

PDB-3nx8:
human cAMP dependent protein kinase in complex with phenol
Method: X-RAY DIFFRACTION / Resolution: 2.0 Å

PDB-3pcz:
Endothiapepsin in complex with benzamidine
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-3prs:
Endothiapepsin in complex with ritonavir
Method: X-RAY DIFFRACTION / Resolution: 1.38 Å

PDB-3pvk:
Secreted aspartic protease 2 in complex with benzamidine
Method: X-RAY DIFFRACTION / Resolution: 1.27 Å

PDB-3pww:
Endothiapepsin in complex with saquinavir
Method: X-RAY DIFFRACTION / Resolution: 1.22 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-CA:
Unknown entry

ChemComp-ANL:
ANILINE / Aniline

ChemComp-IPA:
ISOPROPYL ALCOHOL / alkaloid*YM / Isopropyl alcohol

ChemComp-GOL:
GLYCEROL / Glycerol

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

ChemComp-HOH:
WATER / Water

ChemComp-B3R:
3-bromophenol / Monobromophenol

ChemComp-URE:
UREA / Urea

ChemComp-NMU:
N-METHYLUREA

ChemComp-PGO:
S-1,2-PROPANEDIOL / Propanediol

ChemComp-MN:
Unknown entry

ChemComp-CL:
Unknown entry / Chloride

ChemComp-PGR:
R-1,2-PROPANEDIOL

ChemComp-BXA:
bromoacetic acid / Bromoacetic acid

ChemComp-IPH:
PHENOL / Phenol

ChemComp-BEN:
BENZAMIDINE / Benzamidine

ChemComp-RIT:
RITONAVIR / medication, antiretroviral*YM / Ritonavir

ChemComp-1PE:
PENTAETHYLENE GLYCOL / precipitant*YM / Polyethylene glycol

ChemComp-PGE:
TRIETHYLENE GLYCOL / Polyethylene glycol

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

ChemComp-IMD:
IMIDAZOLE / Imidazole

ChemComp-ROC:
(2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 / medication, antiretroviral*YM / Saquinavir

Source
  • bacillus thermoproteolyticus (bacteria)
  • streptomyces rubiginosus (bacteria)
  • escherichia coli (E. coli)
  • homo sapiens (human)
  • cryphonectria parasitica (chestnut blight fungus)
  • candida albicans (yeast)
KeywordsHYDROLASE / PROTEASE / Aniline / Fragement soaking / Fragment based lead discovery / METALLOPROTEASE / Metal-binding / Secreted / Zymogen / Fragment soaking / 3-Bromophenol / Urea / N-methylurea / S-1 / 2-Propandiol / ISOMERASE / INTRAMOLECULAR OXIDOREDUCTSE / TIM BARREL-BETA-ALPHA-BARRELS / TWO METAL BINDING ITES / Manganese / TRANSFERASE / YGBP / CYTIDYLYLTRANSFERASE / DEOXYXYLULOSE-5-PHOSPHATE PATHWAY (DXP) / ISOPRENOID BIOSYNTHESIS / 1 / 2-Propanediol / FBLD / 2-Bromoacetate / Fragment-based lead discovery / ATP Binding / Phosphorylation / HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex

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