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Structure paper

TitleRescoring docking hit lists for model cavity sites: predictions and experimental testing.
Journal, issue, pagesJ. Mol. Biol., Vol. 377, Page 914-934, Year 2008
Publish dateSep 17, 2007 (structure data deposition date)
AuthorsGraves, A.P. / Shivakumar, D.M. / Boyce, S.E. / Jacobson, M.P. / Case, D.A. / Shoichet, B.K.
External linksJ. Mol. Biol. / PubMed:18280498
MethodsX-ray diffraction
Resolution1.24 - 2.49 Å
Structure data

PDB-2ray:
beta-chlorophenetole in complex with T4 lysozyme L99A
Method: X-RAY DIFFRACTION / Resolution: 1.798 Å

PDB-2raz:
4-(methylthio)nitrobenzene in complex with T4 lysozyme L99A
Method: X-RAY DIFFRACTION / Resolution: 1.641 Å

PDB-2rb0:
2,6-difluorobenzylbromide complex with T4 lysozyme L99A
Method: X-RAY DIFFRACTION / Resolution: 1.84 Å

PDB-2rb1:
2-ethoxyphenol in complex with T4 lysozyme L99A
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-2rb2:
3-methylbenzylazide in complex with T4 lysozyme L99A
Method: X-RAY DIFFRACTION / Resolution: 1.463 Å

PDB-2rbn:
N-phenylglycinonitrile in complex with T4 lysozyme L99A/M102Q
Method: X-RAY DIFFRACTION / Resolution: 1.29 Å

PDB-2rbo:
2-nitrothiophene in complex with T4 lysozyme L99A/M102Q
Method: X-RAY DIFFRACTION / Resolution: 1.29 Å

PDB-2rbp:
2-(n-propylthio)ethanol in complex with T4 lysozyme L99A/M102Q
Method: X-RAY DIFFRACTION / Resolution: 1.467 Å

PDB-2rbq:
3-methylbenzylazide in complex with T4 L99A/M102Q
Method: X-RAY DIFFRACTION / Resolution: 1.633 Å

PDB-2rbr:
2-phenoxyethanol in complex with T4 lysozyme L99A/M102Q
Method: X-RAY DIFFRACTION / Resolution: 1.433 Å

PDB-2rbs:
(r)(+)-3-chloro-1-phenyl-1-propanol in complex with T4 lysozyme L99A/M102Q
Method: X-RAY DIFFRACTION / Resolution: 1.557 Å

PDB-2rbt:
n-methylbenzylamine in complex with Cytochrome C Peroxidase W191G
Method: X-RAY DIFFRACTION / Resolution: 1.24 Å

PDB-2rbu:
Cytochrome C Peroxidase in complex with cyclopentane-carboximidamide
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-2rbv:
Cytochrome C Peroxidase in complex with (1-methyl-1h-pyrrol-2-yl)-methylamine
Method: X-RAY DIFFRACTION / Resolution: 1.39 Å

PDB-2rbw:
Cytochrome C Peroxidase W191G in complex with 1,2-dimethyl-1h-pyridin-5-amine
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-2rbx:
Cytochrome C Peroxidase W191G in complex with pyrimidine-2,4,6-triamine.
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-2rby:
1-methyl-5-imidazolecarboxaldehyde in complex with Cytochrome C Peroxidase W191G
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-2rbz:
Cytochrome C Peroxidase W191G in complex 3-methoxypyridine
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-2rc0:
Cytochrome C Peroxidase W191G in complex with 2-imino-4-methylpiperdine
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-2rc1:
Cytochrome C Peroxidase W191G in complex with 2,4,5-trimethyl-3-oxazoline
Method: X-RAY DIFFRACTION / Resolution: 2.49 Å

PDB-2rc2:
Cytochrome C Peroxidase W191G in complex with 1-methyl-2-vinyl-pyridinium
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

Chemicals

ChemComp-PO4:
PHOSPHATE ION / Phosphate

ChemComp-258:
(2-chloroethoxy)benzene

ChemComp-HOH:
WATER / Water

ChemComp-259:
1-(methylsulfanyl)-4-nitrobenzene

ChemComp-260:
2-(bromomethyl)-1,3-difluorobenzene

ChemComp-261:
2-ethoxyphenol

ChemComp-263:
1-(azidomethyl)-3-methylbenzene

ChemComp-264:
(phenylamino)acetonitrile

ChemComp-265:
2-nitrothiophene

ChemComp-266:
2-(propylsulfanyl)ethanol

ChemComp-268:
2-phenoxyethanol / Phenoxyethanol

ChemComp-269:
(1R)-3-chloro-1-phenylpropan-1-ol

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

ChemComp-271:
N-methyl-1-phenylmethanamine

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

ChemComp-273:
cyclopentanecarboximidamide

ChemComp-278:
1-(1-methyl-1H-pyrrol-2-yl)methanamine

ChemComp-275:
5-amino-1,2-dimethylpyridinium

ChemComp-3AY:
PYRIMIDINE-2,4,6-TRIAMINE

ChemComp-280:
1-methyl-1H-imidazole-5-carbaldehyde

ChemComp-282:
3-methoxypyridine

ChemComp-284:
(4S)-4-methyl-1,4,5,6-tetrahydropyridin-2-amine

ChemComp-285:
(2R,4R,5R)-2,4,5-trimethyl-1,3-oxazolidine

ChemComp-286:
2-ethenyl-1-methylpyridinium

Source
  • enterobacteria phage t4 (virus)
  • bacteriophage t4 (virus)
  • saccharomyces cerevisiae (brewer's yeast)
KeywordsHYDROLASE / protein cavities / OXIDOREDUCTASE

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