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Structure paper

TitlePredicting ligand binding affinity with alchemical free energy methods in a polar model binding site.
Journal, issue, pagesJ. Mol. Biol., Vol. 394, Page 747-763, Year 2009
Publish dateJun 11, 2009 (structure data deposition date)
AuthorsBoyce, S.E. / Mobley, D.L. / Rocklin, G.J. / Graves, A.P. / Dill, K.A. / Shoichet, B.K.
External linksJ. Mol. Biol. / PubMed:19782087
MethodsX-ray diffraction
Resolution1.26 - 2.02 Å
Structure data

PDB-3ht6:
2-methylphenol in complex with T4 lysozyme L99A/M102Q
Method: X-RAY DIFFRACTION / Resolution: 1.59 Å

PDB-3ht7:
2-ethylphenol in complex with T4 lysozyme L99A/M102Q
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-3ht8:
5-chloro-2-methylphenol in complex with T4 lysozyme L99A/M102Q
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-3ht9:
2-methoxyphenol in complex with T4 lysozyme L99A/M102Q
Method: X-RAY DIFFRACTION / Resolution: 2.02 Å

PDB-3htb:
2-propylphenol in complex with T4 lysozyme L99A/M102Q
Method: X-RAY DIFFRACTION / Resolution: 1.81 Å

PDB-3htd:
(Z)-Thiophene-2-carboxaldoxime in complex with T4 lysozyme L99A/M102Q
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-3htf:
4-chloro-1h-pyrazole in complex with T4 lysozyme L99A/M102Q
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-3htg:
2-ethoxy-3,4-dihydro-2h-pyran in complex with T4 lysozyme L99A/M102Q
Method: X-RAY DIFFRACTION / Resolution: 1.26 Å

PDB-3hu8:
2-ethoxyphenol in complex with T4 lysozyme L99A/M102Q
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-3hu9:
Nitrosobenzene in complex with T4 lysozyme L99A/M102Q
Method: X-RAY DIFFRACTION / Resolution: 1.46 Å

PDB-3hua:
4,5,6,7-tetrahydroindole in complex with T4 lysozyme L99A/M102Q
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-3huk:
Benzylacetate in complex with T4 lysozyme L99A/M102Q
Method: X-RAY DIFFRACTION / Resolution: 1.29 Å

PDB-3huq:
Thieno[3,2-b]thiophene in complex with T4 lysozyme L99A/M102Q
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

Chemicals

ChemComp-PO4:
PHOSPHATE ION / Phosphate

ChemComp-JZ0:
o-cresol / O-Cresol

ChemComp-HOH:
WATER / Water

ChemComp-JZ1:
2-ethylphenol

ChemComp-BME:
BETA-MERCAPTOETHANOL / 2-Mercaptoethanol

ChemComp-JZ2:
5-chloro-2-methylphenol

ChemComp-JZ3:
Guaiacol / Guaiacol

ChemComp-JZ4:
2-propylphenol

ChemComp-JZ5:
(NZ)-N-(thiophen-2-ylmethylidene)hydroxylamine

ChemComp-JZ6:
4-chloro-1H-pyrazole

ChemComp-JZ7:
(2S)-2-ethoxy-3,4-dihydro-2H-pyran

ChemComp-261:
2-ethoxyphenol

ChemComp-NBE:
NITROSOBENZENE / Nitrosobenzene

ChemComp-JZ9:
4,5,6,7-tetrahydro-1H-indole

ChemComp-J0Z:
benzyl acetate / Benzyl acetate

ChemComp-J1Z:
thieno[3,2-b]thiophene

Source
  • enterobacteria phage t4 (virus)
KeywordsHYDROLASE / GLYCOSIDASE / BACTERIOLYTIC ENZYME / Antimicrobial

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