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Structure paper

TitleFragments Can Bind Either More Enthalpy or Entropy-Driven: Crystal Structures and Residual Hydration Pattern Suggest Why.
Journal, issue, pagesJ. Med. Chem., Vol. 58, Page 6960-, Year 2015
Publish dateDec 9, 2014 (structure data deposition date)
AuthorsRuehmann, E. / Betz, M. / Heine, A. / Klebe, G.
External linksJ. Med. Chem. / PubMed:26270568
MethodsX-ray diffraction
Resolution1.12 - 1.53 Å
Structure data

PDB-4ud9:
Thrombin in complex with 5-chlorothiophene-2-carboxamide
Method: X-RAY DIFFRACTION / Resolution: 1.124 Å

PDB-4udw:
Thrombin in complex with 1-(2R)-2-amino-3-phenyl-propanoyl-N-(2, 5dichlorophenyl)methylpyrrolidine-2-carboxamide
Method: X-RAY DIFFRACTION / Resolution: 1.16 Å

PDB-4ue7:
Thrombin in complex with 1-amidinopiperidine
Method: X-RAY DIFFRACTION / Resolution: 1.129 Å

PDB-4ueh:
Thrombin in complex with benzamidine
Method: X-RAY DIFFRACTION / Resolution: 1.16 Å

PDB-5af9:
Thrombin in complex with 4-Methoxy-N-(2-pyridinyl)benzamide
Method: X-RAY DIFFRACTION / Resolution: 1.18 Å

PDB-5afy:
Thrombin in complex with 3-chloro-benzamide
Method: X-RAY DIFFRACTION / Resolution: 1.12 Å

PDB-5afz:
Thrombin in complex with (2R)-2-(benzylsulfonylamino)-N-(2-((4- carbamimidoylphenyl)methylamino)-2-oxo-propyl)-3-phenyl-propanamide
Method: X-RAY DIFFRACTION / Resolution: 1.53 Å

PDB-5ahg:
Thrombin in complex with ((4-chlorophenyl)sulfamoyl))diemethylamine
Method: X-RAY DIFFRACTION / Resolution: 1.24 Å

Chemicals

ChemComp-NA:
Unknown entry

ChemComp-PO4:
PHOSPHATE ION / Phosphate

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

ChemComp-GOL:
GLYCEROL / Glycerol

ChemComp-EDO:
1,2-ETHANEDIOL / Ethylene glycol

ChemComp-FQI:
5-CHLORO-2-THIOPHENECARBOXAMIDE

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

ChemComp-HOH:
WATER / Water

ChemComp-N6L:
D-phenylalanyl-N-(2,5-dichlorobenzyl)-L-prolinamide

ChemComp-IOD:
IODIDE ION / Iodide

ChemComp-MRZ:
piperidine-1-carboximidamide

ChemComp-BEN:
BENZAMIDINE / Benzamidine

ChemComp-SJR:
4-methoxy-N-(pyridin-2-yl)benzamide

ChemComp-WCE:
3-CHLORO-BENZAMIDE

ChemComp-UET:
N-(BENZYLSULFONYL)-D-PHENYLALANYL-N-(4-CARBAMIMIDOYLBENZYL)GLYCINAMIDE

ChemComp-Y4L:
((4-Chlorophenyl)sulfamoyl))dimethylamine

Source
  • homo sapiens (human)
  • hirudo medicinalis (medicinal leech)
KeywordsHYDROLASE / HYDROLASE INHIBITOR COMPLEX / SERINE PROTEASE / BLOOD COAGULATION / BLOOD CLOTTING / CONVERTION OF FIBRINOGEN TO FIBRIN / BLOOD CLOTTING INHIBITOR / THROMBIN INHIBITOR / FRAGMENT / GLYCOSYLATION / BLOOD

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