Publications | Structural Genomics Consortium

Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation.

Marcon E, Jain H, Bhattacharya A, Guo H, Phanse S, Pu S, Byram G, Collins BC, Dowdell E, Fenner M, Guo X, Hutchinson A, Kennedy JJ, Krastins B, Larsen B, Lin ZY, Lopez MF, Loppnau P, Miersch S, Nguyen T, Olsen JB, Paduch M, Ravichandran M, Seitova A, Vadali G, Vogelsang MS, Whiteaker JR, Zhong G, Zhong N, Zhao L, Aebersold R, Arrowsmith CH, Emili A, Frappier L, Gingras AC, Gstaiger M, Paulovich AG, Koide S, Kossiakoff AA, Sidhu SS, Wodak SJ, Gräslund S, Greenblatt JF, Edwards AM

Nat. Methods. doi: 10.1038/nmeth.3472

Publication date: June 29, 2015

PMID: 26121405

Structural Basis for the Specificity of Human NUDT16 and Its Regulation by Inosine Monophosphate.

Trésaugues L, Lundbäck T, Welin M, Flodin S, Nyman T, Silvander C, Gräslund S, Nordlund P

PLoS ONE. 10(6):e0131507. doi: 10.1371/journal.pone.0131507

Publication date: June 29, 2015

PMID: 26121039

Mechanisms underlying clinical efficacy of Angiotensin II type 2 receptor (AT2R) antagonist EMA401 in neuropathic pain: clinical tissue and in vitro studies.

Anand U, Yiangou Y, Sinisi M, Fox M, MacQuillan A, Quick T, Korchev YE, Bountra C, McCarthy T, Anand P

Mol Pain. 11(1):38. doi: 10.1186/s12990-015-0038-x

Publication date: June 26, 2015

PMID: 26111701

Biochemical characterization of FIKK8-a unique protein kinase from the malaria parasite Plasmodium falciparum and other apicomplexans.

Osman K, Lou HJ, Qiu W, Brand V, Edwards AM, Turk BE, Hui R

Mol. Biochem. Parasitol.. doi: 10.1016/j.molbiopara.2015.06.002

Publication date: June 22, 2015

PMID: 26112892

Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2.

Sweis RF, Wang Z, Algire M, Arrowsmith CH, Brown PJ, Chiang GG, Guo J, Jakob CG, Kennedy S, Li F, Maag D, Shaw B, Soni NB, Vedadi M, Pappano WN

ACS Med Chem Lett. 6(6):695-700. doi: 10.1021/acsmedchemlett.5b00124

Publication date: June 11, 2015

PMID: 26101576

Tankyrase 1 Inhibitors with Drug-like Properties Identified by Screening a DNA-Encoded Chemical Library.

Samain F, Ekblad T, Mikutis G, Zhong N, Zimmermann M, Nauer A, Bajic D, Decurtins W, Scheuermann J, Brown PJ, Hall J, Gräslund S, Schüler H, Neri D, Franzini RM

J. Med. Chem.. doi: 10.1021/acs.jmedchem.5b00432

Publication date: June 10, 2015

PMID: 26061013

Pim Kinase Inhibitors Evaluated with a Single-Molecule Engineered Nanopore Sensor.

Harrington L, Alexander LT, Knapp S, Bayley H

Angew. Chem. Int. Ed. Engl.. doi: 10.1002/anie.201503141

Publication date: June 8, 2015

PMID: 26058458

Structural Basis of KEAP1 Interactions with Nrf2.

Canning P, Sorrell FJ, Bullock AN

Free Radic. Biol. Med.. doi: 10.1016/j.freeradbiomed.2015.05.034

Publication date: June 6, 2015

PMID: 26057936

MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes.

Stansfeld PJ, Goose JE, Caffrey M, Carpenter EP, Parker JL, Newstead S, Sansom MS

Structure. doi: 10.1016/j.str.2015.05.006

Publication date: May 28, 2015

PMID: 26073602

Kinetic characterization of human histone H3 lysine 36 methyltransferases, ASH1L and SETD2.

Eram MS, Kuznetsova E, Li F, Lima-Fernandes E, Kennedy S, Chau I, Arrowsmith CH, Schapira M, Vedadi M

Biochim. Biophys. Acta. doi: 10.1016/j.bbagen.2015.05.013

Publication date: May 19, 2015

PMID: 26002201

LP99: Discovery and Synthesis of the First Selective BRD7/9 Bromodomain Inhibitor.

Clark PG, Vieira LC, Tallant C, Fedorov O, Singleton DC, Rogers CM, Monteiro OP, Bennett JM, Baronio R, Müller S, Daniels DL, Méndez J, Knapp S, Brennan PE, Dixon DJ

Angew Chem Weinheim Bergstr Ger. 127(21):6315-6319. doi: 10.1002/ange.201501394

Publication date: May 18, 2015

PMID: 27346896

Discovery of a Chemical Tool Inhibitor Targeting the Bromodomains of TRIM24 and BRPF.

Bennett JM, Fedorov O, Tallant C, Monteiro OP, Meier J, Gamble V, Savitski P, Nunez-Alonso GA, Haendler B, Rogers C, Brennan PE, Müller S, Knapp S

J. Med. Chem.. doi: 10.1021/acs.jmedchem.5b00458

Publication date: May 14, 2015

PMID: 25974391

Structural diversity of the epigenetics pocketome.

Cabaye A, Nguyen KT, Liu L, Pande V, Schapira M

Proteins. doi: 10.1002/prot.24830

Publication date: May 13, 2015

PMID: 25974248

Crystal structure of the Bloom's syndrome helicase indicates a role for the HRDC domain in conformational changes.

Newman JA, Savitsky P, Allerston CK, Bizard AH, Özer Ö, Sarlós K, Liu Y, Pardon E, Steyaert J, Hickson ID, Gileadi O

Nucleic Acids Res.. doi: 10.1093/nar/gkv373

Publication date: April 21, 2015

PMID: 25901030

Solution-state NMR structure of the putative morphogene protein BolA (PFE0790c) from Plasmodium falciparum.

Buchko GW, Yee A, Semesi A, Myler PJ, Arrowsmith CH, Hui R

Acta Crystallogr F Struct Biol Commun. 71(Pt 5):514-21. doi: 10.1107/S2053230X1402799X

Publication date: April 18, 2015

PMID: 25945703

LP99: Discovery and Synthesis of the First Selective BRD7/9 Bromodomain Inhibitor.

Clark PG, Vieira LC, Tallant C, Fedorov O, Singleton DC, Rogers CM, Monteiro OP, Bennett JM, Baronio R, Müller S, Daniels DL, Méndez J, Knapp S, Brennan PE, Dixon DJ

Angew. Chem. Int. Ed. Engl.. doi: 10.1002/anie.201501394

Publication date: April 13, 2015

PMID: 25864491

Structures of the Ets Domains of Transcription Factors ETV1, ETV4, ETV5 and FEV: Determinants of DNA Binding and Redox Regulation by Disulfide bond formation.

Cooper CD, Newman JA, Aitkenhead H, Allerston CK, Gileadi O

J. Biol. Chem.. doi: 10.1074/jbc.M115.646737

Publication date: April 12, 2015

PMID: 25866208

Discovery of a Dual PRMT5-PRMT7 Inhibitor.

Smil D, Eram MS, Li F, Kennedy S, Szewczyk MM, Brown PJ, Barsyte-Lovejoy D, Arrowsmith CH, Vedadi M, Schapira M

ACS Med Chem Lett. 6(4):408-12. doi: 10.1021/ml500467h

Publication date: April 9, 2015

PMID: 25893041

Perspective on Computational and Structural Aspects of Kinase Discovery from IPK2014.

Martin E, Knapp S, Engh RA, Moebitz H, Varin T, Roux B, Meiler J, Berdini V, Baumann A, Vieth M

Biochim. Biophys. Acta. doi: 10.1016/j.bbapap.2015.03.014

Publication date: April 7, 2015

PMID: 25861861

Epigenetic targets and drug discovery Part 2: Histone demethylation and DNA methylation.

Liu K, Liu Y, Lau JL, Min J

Pharmacol. Ther.. doi: 10.1016/j.pharmthera.2015.04.001

Publication date: April 6, 2015

PMID: 25857453

Structural and evolutionary divergence of cyclic nucleotide binding domains in eukaryotic pathogens: Implications for drug design.

Mohanty S, Kennedy EJ, Herberg FW, Hui R, Taylor SS, Langsley G, Kannan N

Biochim. Biophys. Acta. doi: 10.1016/j.bbapap.2015.03.012

Publication date: April 3, 2015

PMID: 25847873

LLY-507, a Cell-Active, Potent and Selective Inhibitor of Protein Lysine Methyltransferase SMYD2.

Nguyen H, Allali-Hassani A, Antonysamy S, Chang S, Chen LH, Curtis C, Emtage S, Fan L, Gheyi T, Li F, Liu S, Martin JR, Mendel D, Olsen JB, Pelletier L, Shatseva T, Wu S, Zhang FF, Arrowsmith CH, Brown PJ, Campbell RM, Garcia BA, Barsyte-Lovejoy D, Mader M, Vedadi M

J. Biol. Chem.. doi: 10.1074/jbc.M114.626861

Publication date: March 30, 2015

PMID: 25825497

Selective inhibitors of Cyclin-G associated kinase (GAK) as anti-HCV agents.

Kovackova S, Chang L, Bekerman E, Neveu G, Barouch-Bentov R, Chaikuad A, Heroven C, Sala M, De Jonghe SC, Knapp S, Einav S, Herdewijn P

J. Med. Chem.. doi: 10.1021/jm501759m

Publication date: March 30, 2015

PMID: 25822739

Discovery and characterization of GSK2801, a selective chemical probe for the bromodomains BAZ2A and BAZ2B.

Chen P, Chaikuad A, Bamborough P, Bantscheff M, Bountra C, Chung CW, Fedorov O, Grandi P, Jung D, Lesniak R, Lindon M, Müller S, Philpott M, Prinjha RK, Rogers CM, Selenski C, Tallant C, Werner T, Willson TM, Knapp S, Drewry DH

J. Med. Chem.. doi: 10.1021/acs.jmedchem.5b00209

Publication date: March 23, 2015

PMID: 25799074

Human RECQ1 helicase-driven DNA unwinding, annealing, and branch migration: Insights from DNA complex structures.

Pike AC, Gomathinayagam S, Swuec P, Berti M, Zhang Y, Schnecke C, Marino F, von Delft F, Renault L, Costa A, Gileadi O, Vindigni A

Proc. Natl. Acad. Sci. U.S.A.. doi: 10.1073/pnas.1417594112

Publication date: March 23, 2015

PMID: 25831490

K2P channel gating mechanisms revealed by structures of TREK-2 and a complex with Prozac.

Dong YY, Pike AC, Mackenzie A, McClenaghan C, Aryal P, Dong L, Quigley A, Grieben M, Goubin S, Mukhopadhyay S, Ruda GF, Clausen MV, Cao L, Brennan PE, Burgess-Brown NA, Sansom MS, Tucker SJ, Carpenter EP

Science. 347(6227):1256-1259. doi: 10.1126/science.1261512

Publication date: March 13, 2015

PMID: 25766236

10-Iodo-11H-indolo[3,2-c]quinoline-6-carboxylic Acids Are Selective Inhibitors of DYRK1A.

Falke H, Chaikuad A, Becker A, Loaëc N, Lozach O, Abu Jhaisha S, Becker W, Jones PG, Preu L, Baumann K, Knapp S, Meijer L, Kunick C

J. Med. Chem.. doi: 10.1021/jm501994d

Publication date: March 2, 2015

PMID: 25730262

A Potent, Selective and Cell-Active Allosteric Inhibitor of Protein Arginine Methyltransferase 3 (PRMT3).

Kaniskan HÜ, Szewczyk MM, Yu Z, Eram MS, Yang X, Schmidt K, Luo X, Dai M, He F, Zang I, Lin Y, Kennedy S, Li F, Dobrovetsky E, Dong A, Smil D, Min SJ, Landon M, Lin-Jones J, Huang XP, Roth BL, Schapira M, Atadja P, Barsyte-Lovejoy D, Arrowsmith CH, Brown PJ, Zhao K, Jin J, Vedadi M

Angew. Chem. Int. Ed. Engl.. doi: 10.1002/anie.201412154

Publication date: February 27, 2015

PMID: 25728001

Ankyrin Repeats of ANKRA2 Recognize a PxLPxL Motif on the 3M Syndrome Protein CCDC8.

Nie J, Xu C, Jin J, Aka JA, Tempel W, Nguyen V, You L, Weist R, Min J, Pawson T, Yang XJ

Structure. doi: 10.1016/j.str.2015.02.001

Publication date: February 26, 2015

PMID: 25752541

Structure Enabled Design of BAZ2-ICR, A Chemical Probe Targeting the Bromodomains of BAZ2A and BAZ2B.

Drouin L, McGrath S, Vidler LR, Chaikuad A, Monteiro O, Tallant C, Philpott M, Rogers C, Fedorov O, Liu M, Akhtar W, Hayes A, Raynaud F, Müller S, Knapp S, Hoelder S

J. Med. Chem.. doi: 10.1021/jm501963e

Publication date: February 26, 2015

PMID: 25719566

Building a roadmap for developing combination therapies for Alzheimer's disease.

Perry D, Sperling R, Katz R, Berry D, Dilts D, Hanna D, Salloway S, Trojanowski JQ, Bountra C, Krams M, Luthman J, Potkin S, Gribkoff V, Temple R, Wang Y, Carrillo MC, Stephenson D, Snyder H, Liu E, Ware T, McKew J, Fields FO, Bain LJ, Bens C

Expert Rev Neurother. 15(3):327-33. doi: 10.1586/14737175.2015.996551

Publication date: February 25, 2015

PMID: 25708309

The 9H-purine scaffold reveals induced-fit pocket plasticity of the BRD9 bromodomain.

Picaud S, Strocchia M, Terracciano S, Lauro G, Méndez J, Daniels DL, Riccio R, Bifulco G, Bruno I, Filippakopoulos P

J. Med. Chem.. doi: 10.1021/jm501893k

Publication date: February 22, 2015

PMID: 25703523

Preclinical target validation using patient-derived cells.

Edwards AM, Arrowsmith CH, Bountra C, Bunnage ME, Feldmann M, Knight JC, Patel DD, Prinos P, Taylor MD, Sundström M, Barker P, Barsyte D, Bengtson MH, Bell C, Bowness P, Boycott KM, Buser-Doepner C, Carpenter CL, Carr AJ, Clark K, Das AM, Dhanak D, Dirks P, Ellis J, Fantin VR, Flores C, Fon EA, Frail DE, Gileadi O, O'Hagan RC, Howe T, Isaac JT, Jabado N, Jakobsson PJ, Klareskog L, Knapp S, Lee WH, Lima-Fernandes E, Lundberg IE, Marshall J, Massirer KB, MacKenzie AE, Maruyama T, Mueller-Fahrnow A, Muthuswamy S, Nanchahal J, O'Brien C, Oppermann U, Ostermann N, Petrecca K, Pollock BG, Poupon V, Prinjha RK, Rosenberg SH, Rouleau G, Skingle M, Slutsky AS, Smith GA, Verhelle D, Widmer H, Young LT

Nat Rev Drug Discov. 14(3):149-50. doi: 10.1038/nrd4565

Publication date: February 20, 2015

PMID: 25722227

Structural Insights into the Auto-regulation and Cooperativity of the Human Transcription Factor Ets-2.

Newman JA, Cooper CD, Aitkenhead H, Gileadi O

J. Biol. Chem.. doi: 10.1074/jbc.M114.619270

Publication date: February 10, 2015

PMID: 25670864

Identification of Structure-Activity Relationships from Screening a Structurally Compact DNA-Encoded Chemical Library.

Franzini RM, Ekblad T, Zhong N, Wichert M, Decurtins W, Nauer A, Zimmermann M, Samain F, Scheuermann J, Brown PJ, Hall J, Gräslund S, Schüler H, Neri D

Angew. Chem. Int. Ed. Engl.. doi: 10.1002/anie.201410736

Publication date: February 3, 2015

PMID: 25650139

Human prostaglandin reductase 1 (PGR1): Substrate specificity, inhibitor analysis and site-directed mutagenesis.

Mesa J, Alsina C, Oppermann U, Parés X, Farrés J, Porté S

Chem. Biol. Interact.. doi: 10.1016/j.cbi.2015.01.021

Publication date: January 22, 2015

PMID: 25619643

Clinical Utility Gene Card for: Fibrodysplasia ossificans progressiva.

Bravenboer N, Micha D, Triffit JT, Bullock AN, Ravazollo R, Bocciardi R, di Rocco M, Netelenbos JC, Ten Dijke P, Sánchez-Duffhues G, Kaplan FS, Shore EM, Pignolo RJ, Seemann P, Ventura F, Beaujat G, Eekhoff EM, Pals G

Eur. J. Hum. Genet.. doi: 10.1038/ejhg.2014.274

Publication date: January 21, 2015

PMID: 25604857

Bisubstrate Inhibitor Approach for Targeting Mitotic Kinase Haspin.

Kestav K, Lavogina D, Raidaru G, Chaikuad A, Knapp S, Uri A

Bioconjug. Chem.. doi: 10.1021/bc500464r

Publication date: January 16, 2015

PMID: 25595038

Identification of a Fragment-like Small Molecule Ligand for the Methyl-lysine Binding Protein, 53BP1.

Perfetti MT, Baughman BM, Dickson BM, Mu Y, Cui G, Mader P, Dong A, Norris JL, Rothbart SB, Strahl BD, Brown PJ, Janzen WP, Arrowsmith CH, Mer G, McBride KM, James LI, Frye SV

ACS Chem. Biol.. doi: 10.1021/cb500956g

Publication date: January 15, 2015

PMID: 25590533

Lysine Demethylase KDM4A Associates with Translation Machinery and Regulates Protein Synthesis.

Van Rechem C, Black JC, Boukhali M, Aryee MJ, Graslund S, Haas W, Benes CH, Whetstine JR

Cancer Discov. doi: 10.1158/2159-8290.CD-14-1326

Publication date: January 6, 2015

PMID: 25564516

A small molecule targeting ALK1 prevents Notch cooperativity and inhibits functional angiogenesis.

Kerr G, Sheldon H, Chaikuad A, Alfano I, von Delft F, Bullock AN, Harris AL

Angiogenesis. doi: 10.1007/s10456-014-9457-y

Publication date: January 4, 2015

PMID: 25557927

Structure-activity relationship studies of SETD8 inhibitors.

Ma A, Yu W, Xiong Y, Butler KV, Brown PJ, Jin J

Medchemcomm. 5(12):1892-1898. doi: 10.1039/C4MD00317A

Publication date: January 3, 2015

PMID: 25554733

SPOTing Acetyl-Lysine Dependent Interactions.

Picaud S, Filippakopoulos P

Microarrays (Basel). 4(3):370-88. doi: 10.3390/microarrays4030370

Publication date: January 1, 2015

PMID: 27600229

Purification and interaction analyses of two human lysosomal vitamin B12 transporters: LMBD1 and ABCD4.

Deme JC, Hancock MA, Xia X, Shintre CA, Plesa M, Kim JC, Carpenter EP, Rosenblatt DS, Coulton JW

Mol. Membr. Biol.. 31(7-8):250-61. doi: 10.3109/09687688.2014.990998

Publication date: December 24, 2014

PMID: 25535791

Recombinant renewable polyclonal antibodies.

Ferrara F, D'Angelo S, Gaiotto T, Naranjo L, Tian H, Gräslund S, Dobrovetsky E, Hraber P, Lund-Johansen F, Saragozza S, Sblattero D, Kiss C, Bradbury AR

MAbs. doi: 10.4161/19420862.2015.989047

Publication date: December 20, 2014

PMID: 25530082

Identification of 2,4-diamino-6,7-dimethoxyquinoline derivatives as G9a inhibitors†Electronic supplementary information (ESI) available. See DOI: 10.1039/c4md00274a.

Srimongkolpithak N, Sundriyal S, Li F, Vedadi M, Fuchter MJ

Medchemcomm. 5(12):1821-1828. doi: 10.1039/c4md00274a

Publication date: December 19, 2014

PMID: 25750706

Structural biology and chemistry of protein arginine methyltransferases.

Schapira M, Ferreira de Freitas R

Medchemcomm. 5(12):1779-1788. doi: 10.1039/c4md00269e

Publication date: December 19, 2014

PMID: 26693001

Molecular Basis of Histone Tail Recognition by Human TIP5 PHD Finger and Bromodomain of the Chromatin Remodeling Complex NoRC.

Tallant C, Valentini E, Fedorov O, Overvoorde L, Ferguson FM, Filippakopoulos P, Svergun DI, Knapp S, Ciulli A

Structure. doi: 10.1016/j.str.2014.10.017

Publication date: December 18, 2014

PMID: 25533489

Application of in situ diffraction in high-throughput structure determination platforms.

Aller P, Sanchez-Weatherby J, Foadi J, Winter G, Lobley CM, Axford D, Ashton AW, Bellini D, Brandao-Neto J, Culurgioni S, Douangamath A, Duman R, Evans G, Fisher S, Flaig R, Hall DR, Lukacik P, Mazzorana M, McAuley KE, Mykhaylyk V, Owen RL, Paterson NG, Romano P, Sandy J, Sorensen T, von Delft F, Wagner A, Warren A, Williams M, Stuart DI, Walsh MA

Methods Mol. Biol.. 1261:233-53. doi: 10.1007/978-1-4939-2230-7_13

Publication date: December 17, 2014

PMID: 25502203

Towards a systematic analysis of human short-chain dehydrogenases/reductases (SDR): ligand identification and structure-activity relationships.

Bhatia C, Oerum S, Bray J, Kavanagh KL, Shafqat N, Yue W, Oppermann U

Chem. Biol. Interact.. doi: 10.1016/j.cbi.2014.12.013

Publication date: December 16, 2014

PMID: 25526675