Publications | Structural Genomics Consortium

Crystal Structure of Sphingosine Kinase 1 with PF-543.

Wang J, Knapp S, Pyne NJ, Pyne S, Elkins JM

ACS Med Chem Lett. 5(12):1329-33. doi: 10.1021/ml5004074

Publication date: December 11, 2014

PMID: 25516793

CSB interacts with SNM1A and promotes DNA interstrand crosslink processing.

Iyama T, Lee SY, Berquist BR, Gileadi O, Bohr VA, Seidman MM, McHugh PJ, Wilson DM

Nucleic Acids Res.. doi: 10.1093/nar/gku1279

Publication date: December 10, 2014

PMID: 25505141

BAZ2A (TIP5) is involved in epigenetic alterations in prostate cancer and its overexpression predicts disease recurrence.

Gu L, Frommel SC, Oakes CC, Simon R, Grupp K, Gerig CY, Bär D, Robinson MD, Baer C, Weiss M, Gu Z, Schapira M, Kuner R, Sültmann H, Provenzano M, Yaspo ML, Brors B, Korbel J, Schlomm T, Sauter G, Eils R, Plass C, Santoro R

Nat. Genet.. doi: 10.1038/ng.3165

Publication date: December 8, 2014

PMID: 25485837

A global assessment of cancer genomic alterations in epigenetic mechanisms.

Shah MA, Denton EL, Arrowsmith CH, Lupien M, Schapira M

Epigenetics Chromatin. 7(1):29. doi: 10.1186/1756-8935-7-29

Publication date: December 4, 2014

PMID: 25484917

Optimisation of a triazolopyridine based histone demethylase inhibitor yields a potent and selective KDM2A (FBXL11) inhibitor.

England KS, Tumber A, Krojer T, Scozzafava G, Ng SS, Daniel M, Szykowska A, Che K, von Delft F, Burgess-Brown NA, Kawamura A, Schofield CJ, Brennan PE

Medchemcomm. 5(12):1879-1886. doi: 10.1039/C4MD00291A

Publication date: December 1, 2014

PMID: 26682034

Mechanistic insight into the interaction of BLM helicase with intra-strand G-quadruplex structures.

Chatterjee S, Zagelbaum J, Savitsky P, Sturzenegger A, Huttner D, Janscak P, Hickson ID, Gileadi O, Rothenberg E

Nat Commun. 5:5556. doi: 10.1038/ncomms6556

Publication date: November 25, 2014

PMID: 25418155

Nanog requires BRD4 to maintain murine embryonic stem cell pluripotency and is suppressed by bromodomain inhibitor JQ1 together with Lefty1.

Horne G, Stewart H, Dickson J, Knapp S, Ramsahoye B, Chevassut T

Stem Cells Dev.. doi: 10.1089/scd.2014.0302

Publication date: November 13, 2014

PMID: 25393219

Selective inhibition of EZH2 and EZH1 enzymatic activity by a small molecule suppresses MLL-rearranged leukemia.

Xu B, On DM, Ma A, Parton T, Konze KD, Pattenden SG, Allison DF, Cai L, Rockowitz S, Liu S, Liu Y, Li F, Vedadi M, Frye SV, Garcia BA, Zheng D, Jin J, Wang GG

Blood. doi: 10.1182/blood-2014-06-581082

Publication date: November 13, 2014

PMID: 25395428

The Humoral Immune Response to HCV: Understanding is Key to Vaccine Development.

Cashman SB, Marsden BD, Dustin LB

Front Immunol. 5:550. doi: 10.3389/fimmu.2014.00550

Publication date: November 10, 2014

PMID: 25426115

Identification and Characterization of a Small-Molecule Inhibitor of Death-Associated Protein Kinase 1.

Wilbek TS, Skovgaard T, Sorrell FJ, Knapp S, Berthelsen J, Strømgaard K

Chembiochem. doi: 10.1002/cbic.201402512

Publication date: November 7, 2014

PMID: 25382253

Small Molecules Dorsomorphin and LDN-193189 Inhibit Myostatin/GDF8 Signaling and Promote Functional Myoblast Differentiation.

Horbelt D, Boergermann JH, Chaikuad A, Alfano I, Williams E, Lukonin I, Timmel T, Bullock AN, Knaus P

J. Biol. Chem.. doi: 10.1074/jbc.M114.604397

Publication date: November 3, 2014

PMID: 25368322

Structure and function of dioxygenases in histone demethylation and DNA/RNA demethylation.

Dong C, Zhang H, Xu C, Arrowsmith CH, Min J

IUCrJ. 1(Pt 6):540-549. doi: 10.1107/S2052252514020922

Publication date: November 1, 2014

PMID: 25485134

X-ray Structure of a Hg2+ Complex of Mercuric Reductase (MerA) and QM/MM Study of Hg2+ Transfer between the C-terminal and Buried Catalytic Site Cysteine Pairs.

Lian P, Guo HB, Riccardi D, Dong A, Parks JM, Xu Q, Pai EF, Miller SM, Wei DQ, Smith JC, Guo H

Biochemistry. doi: 10.1021/bi500608u

Publication date: October 24, 2014

PMID: 25343681

Inter-Domain Communication Of Human Cystathionine Beta Synthase: Structural Basis Of S-Adenosyl-L-Methionine Activation.

McCorvie TJ, Kopec J, Hyung SJ, Fitzpatrick F, Feng X, Termine D, Strain-Damerell C, Vollmar M, Fleming J, Janz JM, Bulawa C, Yue WW

J. Biol. Chem.. doi: 10.1074/jbc.M114.610782

Publication date: October 21, 2014

PMID: 25336647

Expanding the clinical and molecular spectrum of thiamine pyrophosphokinase deficiency: A treatable neurological disorder caused by TPK1 mutations.

Banka S, de Goede C, Yue WW, Morris AA, von Bremen B, Chandler KE, Feichtinger RG, Hart C, Khan N, Lunzer V, Mataković L, Marquardt T, Makowski C, Prokisch H, Debus O, Nosaka K, Sonwalkar H, Zimmermann FA, Sperl W, Mayr JA

Mol. Genet. Metab.. doi: 10.1016/j.ymgme.2014.09.010

Publication date: October 5, 2014

PMID: 25458521

Kruidenier et al. reply.

Kruidenier L, Chung CW, Cheng Z, Liddle J, Che K, Joberty G, Bantscheff M, Bountra C, Bridges A, Diallo H, Eberhard D, Hutchinson S, Jones E, Katso R, Leveridge M, Mander PK, Mosley J, Ramirez-Molina C, Rowland P, Schofield CJ, Sheppard RJ, Smith JE, Swales C, Tanner R, Thomas P, Tumber A, Drewes G, Oppermann U, Patel DJ, Lee K, Wilson DM

Nature. 514(7520):E2. doi: 10.1038/nature13689

Publication date: October 1, 2014

PMID: 25279927

Using textons to rank crystallization droplets by the likely presence of crystals.

Ng JT, Dekker C, Kroemer M, Osborne M, von Delft F

Acta Crystallogr. D Biol. Crystallogr.. 70(Pt 10):2702-18. doi: 10.1107/S1399004714017581

Publication date: October 1, 2014

PMID: 25286854

Structure and function of the nucleosome-binding PWWP domain.

Qin S, Min J

Trends Biochem. Sci.. doi: 10.1016/j.tibs.2014.09.001

Publication date: September 29, 2014

PMID: 25277115

OOMMPPAA: A tool to aid directed synthesis by the combined analysis of activity and structural data.

Bradley A, Wall I, Green D, Deane CM, Marsden B

J Chem Inf Model. doi: 10.1021/ci500245d

Publication date: September 22, 2014

PMID: 25244105

Structural basis for selective binding of m(6)A RNA by the YTHDC1 YTH domain.

Xu C, Wang X, Liu K, Roundtree IA, Tempel W, Li Y, Lu Z, He C, Min J

Nat. Chem. Biol.. doi: 10.1038/nchembio.1654

Publication date: September 21, 2014

PMID: 25242552

Identification and structure-function analysis of sub-family selective G protein-coupled receptor kinase inhibitors.

Homan KT, Larimore KM, Elkins JM, Sklarz M, Knapp S, Tesmer JJ

ACS Chem. Biol.. doi: 10.1021/cb5006323

Publication date: September 19, 2014

PMID: 25238254

A unique inhibitor binding site in ERK1/2 is associated with slow binding kinetics.

Chaikuad A, M C Tacconi E, Zimmer J, Liang Y, Gray NS, Tarsounas M, Knapp S

Nat. Chem. Biol.. doi: 10.1038/nchembio.1629

Publication date: September 7, 2014

PMID: 25195011

The Crystal Structure of the RhoA : AKAP-Lbc DH-PH Domain Complex.

Abdul Azeez KR, Knapp S, Fernandes JM, Klussmann E, Elkins JM

Biochem. J.. doi: 10.1042/BJ20140606

Publication date: September 4, 2014

PMID: 25186459

(R)-PFI-2 is a potent and selective inhibitor of SETD7 methyltransferase activity in cells.

Barsyte-Lovejoy D, Li F, Oudhoff MJ, Tatlock JH, Dong A, Zeng H, Wu H, Freeman SA, Schapira M, Senisterra GA, Kuznetsova E, Marcellus R, Allali-Hassani A, Kennedy S, Lambert JP, Couzens AL, Aman A, Gingras AC, Al-Awar R, Fish PV, Gerstenberger BS, Roberts L, Benn CL, Grimley RL, Braam MJ, Rossi FM, Sudol M, Brown PJ, Bunnage ME, Owen DR, Zaph C, Vedadi M, Arrowsmith CH

Proc. Natl. Acad. Sci. U.S.A.. doi: 10.1073/pnas.1407358111

Publication date: August 18, 2014

PMID: 25136132

ACVR1 Mutations in DIPG: Lessons Learned from FOP.

Taylor KR, Vinci M, Bullock AN, Jones C

Cancer Res.. doi: 10.1158/0008-5472.CAN-14-1298

Publication date: August 18, 2014

PMID: 25136070

Functional Characterization and Categorization of Missense Mutations that Cause Methylmalonyl-CoA Mutase (MUT) Deficiency.

Forny P, Froese DS, Suormala T, Yue WW, Baumgartner MR

Hum. Mutat.. doi: 10.1002/humu.22633

Publication date: August 14, 2014

PMID: 25125334

Lost but making progress-Where will new analgesic drugs come from?

Borsook D, Hargreaves R, Bountra C, Porreca F

Sci Transl Med. 6(249):249sr3. doi: 10.1126/scitranslmed.3008320

Publication date: August 13, 2014

PMID: 25122640

Recently targeted kinases and their inhibitors-the path to clinical trials.

Knapp S, Sundström M

Curr Opin Pharmacol. 17C:58-63. doi: 10.1016/j.coph.2014.07.015

Publication date: August 8, 2014

PMID: 25113945

Structure-activity relationship of 3,5-diaryl-2-aminopyridine ALK2 inhibitors reveals unaltered binding affinity for fibrodysplasia ossificans progressiva causing mutants.

Mohedas A, Wang Y, Sanvitale CE, Canning P, Choi S, Xing X, Bullock AN, Cuny GD, Yu PB

J. Med. Chem.. doi: 10.1021/jm501177w

Publication date: August 7, 2014

PMID: 25101911

What is the future of bromodomains in targeted drug development?

Fedorov O

Future Med Chem. 6(10):1101-3. doi: 10.4155/fmc.14.64

Publication date: August 1, 2014

PMID: 25078130

Lysine methylation-dependent binding of 53BP1 to the pRb tumor suppressor.

Carr SM, Munro S, Zalmas LP, Fedorov O, Johansson C, Krojer T, Sagum CA, Bedford MT, Oppermann U, La Thangue NB

Proc. Natl. Acad. Sci. U.S.A.. doi: 10.1073/pnas.1403737111

Publication date: July 21, 2014

PMID: 25049398

Corrigendum: Dual kinase-bromodomain inhibitors for rationally designed polypharmacology.

Ciceri P, Müller S, O'Mahony A, Fedorov O, Filippakopoulos P, Hunt JP, Lasater EA, Pallares G, Picaud S, Wells C, Martin S, Wodicka LM, Shah NP, Treiber DK, Knapp S

Nat. Chem. Biol.. 10(8):692.

Publication date: July 18, 2014

PMID: 25036311

Discovery of a Selective, Substrate-competitive Inhibitor of the Lysine Methyltransferase SETD8.

Ma A, Yu W, Li F, Bleich RM, Herold JM, Butler KV, Norris JL, Korboukh V, Tripathy A, Janzen WP, Arrowsmith CH, Frye SV, Vedadi M, Brown PJ, Jin J

J. Med. Chem.. doi: 10.1021/jm500871s

Publication date: July 17, 2014

PMID: 25032507

A Methylation-Phosphorylation Switch Determines Sox2 Stability and Function in ESC Maintenance or Differentiation.

Fang L, Zhang L, Wei W, Jin X, Wang P, Tong Y, Li J, Du JX, Wong J

Mol. Cell. doi: 10.1016/j.molcel.2014.06.018

Publication date: July 16, 2014

PMID: 25042802

Assessing cellular efficacy of bromodomain inhibitors using fluorescence recovery after photobleaching.

Philpott M, Rogers CM, Yapp C, Wells C, Lambert JP, Strain-Damerell C, Burgess-Brown NA, Gingras AC, Knapp S, Müller S

Epigenetics Chromatin. 7:14. doi: 10.1186/1756-8935-7-14

Publication date: July 13, 2014

PMID: 25097667

Human-chromatin-related protein interactions identify a demethylase complex required for chromosome segregation.

Marcon E, Ni Z, Pu S, Turinsky AL, Trimble SS, Olsen JB, Silverman-Gavrila R, Silverman-Gavrila L, Phanse S, Guo H, Zhong G, Guo X, Young P, Bailey S, Roudeva D, Zhao D, Hewel J, Li J, Gräslund S, Paduch M, Kossiakoff AA, Lupien M, Emili A, Wodak SJ, Greenblatt J

Cell Rep. 8(1):297-310. doi: 10.1016/j.celrep.2014.05.050

Publication date: July 10, 2014

PMID: 24981860

Bromodomain Protein BRD4 Is Required for Estrogen Receptor-Dependent Enhancer Activation and Gene Transcription.

Nagarajan S, Hossan T, Alawi M, Najafova Z, Indenbirken D, Bedi U, Taipaleenmäki H, Ben-Batalla I, Scheller M, Loges S, Knapp S, Hesse E, Chiang CM, Grundhoff A, Johnsen SA

Cell Rep. doi: 10.1016/j.celrep.2014.06.016

Publication date: July 9, 2014

PMID: 25017071

A scintillation proximity assay for histone demethylases.

Yu W, Eram MS, Hajian T, Szykowska A, Burgess-Brown N, Vedadi M, Brown PJ

Anal. Biochem.. doi: 10.1016/j.ab.2014.06.023

Publication date: July 8, 2014

PMID: 25010373

RPRD1A and RPRD1B are human RNA polymerase II C-terminal domain scaffolds for Ser5 dephosphorylation.

Ni Z, Xu C, Guo X, Hunter GO, Kuznetsova OV, Tempel W, Marcon E, Zhong G, Guo H, Kuo WH, Li J, Young P, Olsen JB, Wan C, Loppnau P, El Bakkouri M, Senisterra GA, He H, Huang H, Sidhu SS, Emili A, Murphy S, Mosley AL, Arrowsmith CH, Min J, Greenblatt JF

Nat. Struct. Mol. Biol.. doi: 10.1038/nsmb.2853

Publication date: July 6, 2014

PMID: 24997600

Discovery and Optimization of Small-Molecule Ligands for the CBP/p300 Bromodomains.

Hay DA, Fedorov O, Martin S, Singleton DC, Tallant C, Wells C, Picaud S, Philpott M, Monteiro OP, Rogers CM, Conway SJ, Rooney TP, Tumber A, Yapp C, Filippakopoulos P, Bunnage ME, Müller S, Knapp S, Schofield CJ, Brennan PE

J. Am. Chem. Soc.. 136(26):9308-19. doi: 10.1021/ja412434f

Publication date: July 2, 2014

PMID: 24946055

Multiparameter Optimization in CNS Drug Discovery: Design of Pyrimido[4,5-d]azepines as Potent 5-Hydroxytryptamine 2C (5-HT2C) Receptor Agonists with Exquisite Functional Selectivity over 5-HT2A and 5-HT2B Receptors.

Storer RI, Brennan PE, Brown AD, Bungay PJ, Conlon KM, Corbett MS, DePianta RP, Fish PV, Heifetz A, Ho DK, Jessiman AS, McMurray G, de Oliveira CA, Roberts LR, Root JA, Shanmugasundaram V, Shapiro MJ, Skerten M, Westbrook D, Wheeler S, Whitlock GA, Wright J

J. Med. Chem.. 57(12):5258-69. doi: 10.1021/jm5003292

Publication date: June 26, 2014

PMID: 24878222

Linking genotypes database with locus-specific database and genotype-phenotype correlation in phenylketonuria.

Wettstein S, Underhaug J, Perez B, Marsden BD, Yue WW, Martinez A, Blau N

Eur. J. Hum. Genet.. doi: 10.1038/ejhg.2014.114

Publication date: June 18, 2014

PMID: 24939588

STRUCTURAL CHARACTERIZATION OF HUMAN CHOLESTEROL 7α-HYDROXYLASE.

Tempel W, Grabovec I, MacKenzie F, Dichenko YV, Usanov SA, Gilep AA, Park HW, Strushkevich N

J. Lipid Res.. doi: 10.1194/jlr.M050765

Publication date: June 13, 2014

PMID: 24927729

A comparison of protein kinases inhibitor screening methods using both enzymatic activity and binding affinity determination.

Rudolf AF, Skovgaard T, Knapp S, Jensen LJ, Berthelsen J

PLoS ONE. 9(6):e98800. doi: 10.1371/journal.pone.0098800

Publication date: June 10, 2014

PMID: 24915177

Structural basis for histone mimicry and hijacking of host proteins by influenza virus protein NS1.

Qin S, Liu Y, Tempel W, Eram MS, Bian C, Liu K, Senisterra G, Crombet L, Vedadi M, Min J

Nat Commun. 5:3952. doi: 10.1038/ncomms4952

Publication date: May 24, 2014

PMID: 24853335

A Series of Potent CREBBP Bromodomain Ligands Reveals an Induced-Fit Pocket Stabilized by a Cation-π Interaction.

Rooney TP, Filippakopoulos P, Fedorov O, Picaud S, Cortopassi WA, Hay DA, Martin S, Tumber A, Rogers CM, Philpott M, Wang M, Thompson AL, Heightman TD, Pryde DC, Cook A, Paton RS, Müller S, Knapp S, Brennan PE, Conway SJ

Angew. Chem. Int. Ed. Engl.. doi: 10.1002/anie.201402750

Publication date: May 12, 2014

PMID: 24821300

Ribosomal oxygenases are structurally conserved from prokaryotes to humans.

Chowdhury R, Sekirnik R, Brissett NC, Krojer T, Ho CH, Ng SS, Clifton IJ, Ge W, Kershaw NJ, Fox GC, Muniz JR, Vollmar M, Phillips C, Pilka ES, Kavanagh KL, von Delft F, Oppermann U, McDonough MA, Doherty AJ, Schofield CJ

Nature. doi: 10.1038/nature13263

Publication date: May 11, 2014

PMID: 24814345

A Chromatin-Dependent Role of the Fragile X Mental Retardation Protein FMRP in the DNA Damage Response.

Alpatov R, Lesch BJ, Nakamoto-Kinoshita M, Blanco A, Chen S, Stützer A, Armache KJ, Simon MD, Xu C, Ali M, Murn J, Prisic S, Kutateladze TG, Vakoc CR, Min J, Kingston RE, Fischle W, Warren ST, Page DC, Shi Y

Cell. 157(4):869-81. doi: 10.1016/j.cell.2014.03.040

Publication date: May 8, 2014

PMID: 24813610

Structural basis for phosphoinositide substrate recognition, catalysis, and membrane interactions in human inositol polyphosphate 5-phosphatases.

Trésaugues L, Silvander C, Flodin S, Welin M, Nyman T, Gräslund S, Hammarström M, Berglund H, Nordlund P

Structure. 22(5):744-55. doi: 10.1016/j.str.2014.01.013

Publication date: May 6, 2014

PMID: 24704254

Human UTY(KDM6C) is a Male-Specific N{epsilon}-Methyl Lysyl-Demethylase.

Walport LJ, Hopkinson RJ, Vollmar M, Madden SK, Gileadi C, Oppermann U, Schofield CJ, Johansson C

J. Biol. Chem.. doi: 10.1074/jbc.M114.555052

Publication date: May 5, 2014

PMID: 24798337