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TitleDetection of Secondary Binding Sites in Proteins Using Fragment Screening.
Journal, issue, pagesProc. Natl. Acad. Sci. USA, Vol. 112, Page 15910-15915, Year 2015
Publish dateNov 27, 2015 (structure data deposition date)
AuthorsLudlow, R.F. / Verdonk, M.L. / Saini, H.K. / Tickle, I.J. / Jhoti, H.
External linksProc. Natl. Acad. Sci. USA / PubMed:26655740
MethodsX-ray diffraction
Resolution1.83 - 2.72 Å
Structure data

PDB-5fp5:
Structure of cyclin-dependent kinase 2 with small-molecule ligand 4- fluorobenzoic acid (AT222) in an alternate binding site.
Method: X-RAY DIFFRACTION / Resolution: 2.16 Å

PDB-5fp6:
Structure of cyclin-dependent kinase 2 with small-molecule ligand 3-(4,7-dichloro-1H-indol-3-yl)prop-2-yn-1-ol (AT17833) in an alternate binding site.
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-5fpd:
Structure of heat shock-related 70kDA protein 2 with small-molecule ligand pyrazine-2-carboxamide (AT513) in an alternate binding site.
Method: X-RAY DIFFRACTION / Resolution: 1.97 Å

PDB-5fpe:
Structure of heat shock-related 70kDA protein 2 with small-molecule ligand 1H-1,2,4-triazol-3-amine (AT485) in an alternate binding site.
Method: X-RAY DIFFRACTION / Resolution: 1.96 Å

PDB-5fpm:
Structure of heat shock-related 70kDA protein 2 with small-molecule ligand 5-phenyl-1,3,4-oxadiazole-2-thiol (AT809) in an alternate binding site.
Method: X-RAY DIFFRACTION / Resolution: 1.96 Å

PDB-5fpn:
Structure of heat shock-related 70kDA protein 2 with small-molecule ligand 3,5-dimethyl-1H-pyrazole-4-carboxylic acid (AT9084) in an alternate binding site.
Method: X-RAY DIFFRACTION / Resolution: 1.96 Å

PDB-5fpo:
Structure of Bacterial DNA Ligase with small-molecule ligand 1H- indazol-7-amine (AT4213) in an alternate binding site.
Method: X-RAY DIFFRACTION / Resolution: 1.83 Å

PDB-5fpr:
Structure of Bacterial DNA Ligase with small-molecule ligand pyrimidin-2-amine (AT371) in an alternate binding site.
Method: X-RAY DIFFRACTION / Resolution: 2.0 Å

PDB-5fps:
Structure of hepatitis C virus (HCV) full-length NS3 complex with small-molecule ligand 3-aminobenzene-1,2-dicarboxylic acid (AT1246) in an alternate binding site.
Method: X-RAY DIFFRACTION / Resolution: 2.68 Å

PDB-5fpt:
Structure of hepatitis C virus (HCV) full-length NS3 complex with small-molecule ligand 2-(1-methyl-1H-indol-3-yl)acetic acid (AT3437) in an alternate binding site.
Method: X-RAY DIFFRACTION / Resolution: 2.72 Å

PDB-5fpy:
Structure of hepatitis C virus (HCV) full-length NS3 complex with small-molecule ligand 5-bromo-1-methyl-1H-indole-2-carboxylic acid (AT21457) in an alternate binding site.
Method: X-RAY DIFFRACTION / Resolution: 2.52 Å

Chemicals

ChemComp-1Y6:
4-fluorobenzoic acid

ChemComp-ACE:
ACETYL GROUP

ChemComp-HOH:
WATER

ChemComp-MFZ:
3-(4,7-dichloro-1H-indol-3-yl)prop-2-yn-1-ol

ChemComp-PZA:
PYRAZINE-2-CARBOXAMIDE / medication*YM

ChemComp-3TR:
3-AMINO-1,2,4-TRIAZOLE / inhibitor*YM

ChemComp-IWT:
5-PHENYL-1,3,4-OXADIAZOLE-2-THIOL

ChemComp-KYD:
3,5-DIMETHYL-1H-PYRAZOLE-4-CARBOXYLIC ACID

ChemComp-10L:
1H-indazol-7-amine

ChemComp-SO4:
SULFATE ION

ChemComp-LGA:
PYRIMIDIN-2-AMINE

ChemComp-UP8:
3-AMINOBENZENE-1,2-DICARBOXYLIC ACID

ChemComp-3VY:
(1-methyl-1H-indol-3-yl)acetic acid

ChemComp-R2N:
5-bromo-1-methyl-1H-indole-2-carboxylic acid

Source
  • homo sapiens (human)
  • staphylococcus aureus (bacteria)
  • hepatitis c virus (isolate bk)
KeywordsTRANSFERASE / KINASE / MITOSIS / CELL CYCLE / FRAGMENT SCREENING / ALTERNATE BINDING SITE. / CHAPERONE / HEAT SHOCK-RELATED PROTEIN / HEAT SHOCK / HSP70 / HSPA2 / PROTEIN-LIGAND COMPLEX / ALTERNATE BINDING SITE / AT513. / AT485. / AT809. / SIGNALING PROTEIN / AT9084. / LIGASE / ANTIBIOTIC DESIGN / AT4213. / AT371. / HYDROLASE / HEPATITIS C VIRUS / HCV / NS3 COMPLEX / PROTEASE-HELICASE / AT1246. / AT3437. / AT21457.

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