메뉴 건너뛰기




Volumn , Issue , 2015, Pages 165-181

Achieving high quality ligand chemistry in protein-ligand crystal structures for drug design

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEXATION; COMPUTATIONAL CHEMISTRY; LIGANDS; PROTEINS; X RAY CRYSTALLOGRAPHY;

EID: 84943372312     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-94-017-9719_13     Document Type: Chapter
Times cited : (3)

References (44)
  • 2
    • 85032519266 scopus 로고    scopus 로고
    • Achieving high quality ligand chemistry in protein x-ray structures. Workshop prepared for the “structural basis of pharmacology: Deeper understanding of drug discovery through crystallography
    • June
    • Smart OS (2014) Achieving high quality ligand chemistry in protein X-ray structures. Workshop prepared for the “Structural Basis of Pharmacology: Deeper Understanding of Drug Discovery through Crystallography”, Meeting Erice June http://grade.globalphasing.org/tut/erice_workshop/
    • (2014) ”, Meeting Erice
    • Smart, O.S.1
  • 4
  • 7
    • 84907829283 scopus 로고    scopus 로고
    • Continuous mutual improvement of macromolecular structure models in the pdb and of x-ray crystallographic software: The dual role of deposited experimental data
    • Buster-report. Global Phasing Ltd, BusterReport
    • Terwilliger TC, Bricogne G (2014) Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data. Acta Crystallogr D Biol Crystallogr 70(10):2533–2543 Buster-report. Global Phasing Ltd. https://www.globalphasing.com/buster/wiki/index.cgi? BusterReport
    • (2014) Acta Crystallogr D Biol Crystallogr , vol.70 , Issue.10 , pp. 2533-2543
    • Terwilliger, T.C.1    Bricogne, G.2
  • 11
    • 0001752768 scopus 로고    scopus 로고
    • The cambridge structural database: A quarter of a million crystal structures and rising
    • Allen FH (2002) The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Crystallogr Sect B Struct Sci 58:380–388
    • (2002) Acta Crystallogr Sect B Struct Sci , vol.58 , pp. 380-388
    • Allen, F.H.1
  • 19
    • 84873572846 scopus 로고    scopus 로고
    • Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structures
    • Pozharski E, Weichenberger CX, Rupp B (2013) Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structures. Acta Crystallogr Sect D: Biol Crystallogr 69:150–167
    • (2013) Acta Crystallogr Sect D: Biol Crystallogr , vol.69 , pp. 150-167
    • Pozharski, E.1    Weichenberger, C.X.2    Rupp, B.3
  • 20
    • 73449126548 scopus 로고    scopus 로고
    • The structural basis for the prevention of nonsteroidal antiinflammatory druginduced gastrointestinal tract damage by the c-lobe of bovine colostrum lactoferrin
    • Mir R, Singh N, Vikram G, Kumar RP, Sinha M, Bhushan A, Kaur P, Srinivasan A, Sharma S, Singh TP (2009) The structural basis for the prevention of nonsteroidal antiinflammatory druginduced gastrointestinal tract damage by the C-lobe of bovine colostrum lactoferrin. Biophys J 97(12):3178–doi:10.1016/j.bpj.2009.09.030
    • (2009) Biophys J , vol.97 , Issue.12
    • Mir, R.1    Singh, N.2    Vikram, G.3    Kumar, R.P.4    Sinha, M.5    Bhushan, A.6    Kaur, P.7    Srinivasan, A.8    Sharma, S.9    Singh, T.P.10
  • 21
    • 52249114682 scopus 로고    scopus 로고
    • Limitations and lessons in the use of x-ray structural information in drug design
    • Davis AM, St-Gallay SA, Kleywegt GJ (2008) Limitations and lessons in the use of X-ray structural information in drug design. Drug Discov Today 13(19–20):831–doi:10.1016/j. drudis.2008.06.006
    • (2008) Drug Discov Today , vol.13 , Issue.1920
    • Davis, A.M.1    St-Gallay, S.A.2    Kleywegt, G.J.3
  • 25
    • 84863097556 scopus 로고    scopus 로고
    • The good, the bad and the twisted: A survey of ligand geometry in protein crystal structures
    • Liebeschuetz J, Hennemann J, Olsson T, Groom CR (2012) The good, the bad and the twisted: a survey of ligand geometry in protein crystal structures. J Comput Aided Mol Des 26(2):169–183
    • (2012) J Comput Aided Mol Des , vol.26 , Issue.2 , pp. 169-183
    • Liebeschuetz, J.1    Hennemann, J.2    Olsson, T.3    Groom, C.R.4
  • 26
  • 27
    • 33750111588 scopus 로고    scopus 로고
    • Pyrrolidine carboxamides as a novel class of inhibitors of enoyl acyl carrier protein reductase from mycobacterium tuberculosis
    • He X, Alian A, Stroud R, de Montellano PRO (2006) Pyrrolidine carboxamides as a novel class of inhibitors of enoyl acyl carrier protein reductase from Mycobacterium tuberculosis. J Med Chem 49(21):6308–6323
    • (2006) J Med Chem , vol.49 , Issue.21 , pp. 6308-6323
    • He, X.1    Alian, A.2    Stroud, R.3    De Montellano, P.4
  • 28
  • 31
    • 0031677841 scopus 로고    scopus 로고
    • Crystal structure of the effectorbinding domain of the trehalose-repressor of escherichia coli, a member of the laci family, in its complexes with inducer trekalose-6-phosphate and noninducer trehalose
    • Hars U, Horlacher R, Boos W, Welte W, Diederichs K (1998) Crystal structure of the effectorbinding domain of the trehalose-repressor of Escherichia coli, a member of the LacI family, in its complexes with inducer trekalose-6-phosphate and noninducer trehalose. Protein Sci 7(12):2511–2521
    • (1998) Protein Sci , vol.7 , Issue.12 , pp. 2511-2521
    • Hars, U.1    Horlacher, R.2    Boos, W.3    Welte, W.4    Diederichs, K.5
  • 33
    • 43349096333 scopus 로고    scopus 로고
    • Using msdchem to search the pdb ligand dictionary. Current protocols in bioinformatics/editorial board
    • Chapter 14:Unit14.13
    • Dimitropoulos D, Ionides J, Henrick K (2006) Using MSDchem to search the PDB ligand dictionary. Current protocols in bioinformatics/editorial board, Andreas D Baxevanis [et al] Chapter 14:Unit14.13
    • (2006) Andreas D Baxevanis [Et Al]
    • Dimitropoulos, D.1    Ionides, J.2    Henrick, K.3
  • 35
    • 0026597444 scopus 로고
    • Free r-value – a novel statistical quantity for assessing the accuracy of crystal-structures
    • Brunger AT (1992) Free R-value – a novel statistical quantity for assessing the accuracy of crystal-structures. Nature 355(6359):472–475
    • (1992) Nature , vol.355 , Issue.6359 , pp. 472-475
    • Brunger, A.T.1
  • 36
    • 0042915882 scopus 로고    scopus 로고
    • The structure of jnk3 in complex with small molecule inhibitors: Structural basis for potency and selectivity
    • Scapin G, Patel SB, Lisnock J, Becker JW, LoGrasso PV (2003) The structure of JNK3 in complex with small molecule inhibitors: structural basis for potency and selectivity. Chem Biol 10(8):705–712
    • (2003) Chem Biol , vol.10 , Issue.8 , pp. 705-712
    • Scapin, G.1    Patel, S.B.2    Lisnock, J.3    Becker, J.W.4    LoGrasso, P.V.5
  • 37
    • 0038336897 scopus 로고    scopus 로고
    • Application and limitations of x-ray crystallographic data in structure-based ligand and drug design
    • Davis AM, Teague SJ, Kleywegt GJ (2003) Application and limitations of X-ray crystallographic data in structure-based ligand and drug design. Angew Chem Int Ed 42(24):2718–2736
    • (2003) Angew Chem Int Ed , vol.42 , Issue.24 , pp. 2718-2736
    • Davis, A.M.1    Teague, S.J.2    Kleywegt, G.J.3
  • 40
    • 78651250896 scopus 로고    scopus 로고
    • Challenges in the determination of the binding modes of nonstandard ligands in x-ray crystal complexes
    • Malde AK, Mark AE (2011) Challenges in the determination of the binding modes of nonstandard ligands in X-ray crystal complexes. J Comput Aided Mol Des 25(1):1–12
    • (2011) J Comput Aided Mol Des , vol.25 , Issue.1 , pp. 1-12
    • Malde, A.K.1    Mark, A.E.2
  • 41
    • 84870308957 scopus 로고    scopus 로고
    • Essential considerations for using protein-ligand structures in drug discovery
    • Warren GL, Do TD, Kelley BP, Nicholls A, Warren SD (2012) Essential considerations for using protein-ligand structures in drug discovery. Drug Discov Today 17(23–24):1270–1281
    • (2012) Drug Discov Today , vol.17 , Issue.23-24 , pp. 1270-1281
    • Warren, G.L.1    Do, T.D.2    Kelley, B.P.3    Nicholls, A.4    Warren, S.D.5
  • 42
    • 84904339885 scopus 로고    scopus 로고
    • Protein-ligand cocrystal structures: We can do better
    • Reynolds CH (2014) Protein-ligand cocrystal structures: we can do better. ACS Med Chem Lett 5(7):727–729
    • (2014) ACS Med Chem Lett , vol.5 , Issue.7 , pp. 727-729
    • Reynolds, C.H.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.