Publications | Structural Genomics Consortium

A p53 Super-tumor Suppressor Reveals a Tumor Suppressive p53-Ptpn14-Yap Axis in Pancreatic Cancer.

Mello SS, Valente LJ, Raj N, Seoane JA, Flowers BM, McClendon J, Bieging-Rolett KT, Lee J, Ivanochko D, Kozak MM, Chang DT, Longacre TA, Koong AC, Arrowsmith CH, Kim SK, Vogel H, Wood LD, Hruban RH, Curtis C, Attardi LD

Cancer Cell. 32(4):460-473.e6. doi: 10.1016/j.ccell.2017.09.007

Publication date: October 9, 2017

PMID: 29017057

Discovery of a selective allosteric inhibitor targeting macrodomain 2 of poly-adenosine-diphosphate-ribose polymerases 14.

Schuller M, Riedel K, Gibbs-Seymour I, Uth K, Sieg C, Gehring AP, Ahel I, Bracher F, Kessler BM, Elkins JM, Knapp S

ACS Chem. Biol.. doi: 10.1021/acschembio.7b00445

Publication date: October 9, 2017

PMID: 28991428

Synthesis and Demonstration of the Biological Relevance of sp(3) -rich Scaffolds Distantly Related to Natural Product Frameworks.

Foley DJ, Craven PGE, Collins PM, Doveston RG, Aimon A, Talon R, Churcher I, von Delft F, Marsden SP, Nelson A

Chemistry. doi: 10.1002/chem.201704169

Publication date: October 6, 2017

PMID: 28983993

Synthesis of kinase inhibitors containing a pentafluorosulfanyl moiety.

Sansook S, Ocasio CA, Day IJ, Tizzard GJ, Coles SJ, Fedorov O, Bennett JM, Elkins JM, Spencer J

Org. Biomol. Chem.. doi: 10.1039/c7ob02289a

Publication date: October 6, 2017

PMID: 28984325

Discovery of a highly selective cell-active inhibitor of KDM2/7.

Gerken P, Wolstenhulme J, Tumber A, Hatch S, Zhang Y, Müller S, Chandler S, Mair B, Li F, Nijman S, Konietzny R, Szommer T, Yapp C, Fedorov O, Benesch J, Vedadi M, Kessler B, Kawamura A, Brennan P, Smith MD

Angew. Chem. Int. Ed. Engl.. doi: 10.1002/anie.201706788

Publication date: October 4, 2017

PMID: 28976073

A systematic analysis of atomic protein-ligand interactions in the PDB.

Ferreira de Freitas R, Schapira M

Medchemcomm. 8(10):1970-1981. doi: 10.1039/c7md00381a

Publication date: October 1, 2017

PMID: 29308120

Correction for Bagarova et al., "Constitutively Active ALK2 Receptor Mutants Require Type II Receptor Cooperation".

Bagarova J, Vonner AJ, Armstrong KA, Börgermann J, Lai CSC, Deng DY, Beppu H, Alfano I, Filippakopoulos P, Morrell NW, Bullock AN, Knaus P, Mishina Y, Yu PB

Mol. Cell. Biol.. 37(19):. doi: 10.1128/MCB.00284-17

Publication date: October 1, 2017

PMID: 28899999

Disease Association and Druggability of WD40 Repeat Proteins.

Song R, Wang ZD, Schapira M

J. Proteome Res.. doi: 10.1021/acs.jproteome.7b00451

Publication date: September 28, 2017

PMID: 28956604

Structural Complexity in the KCTD Family of Cullin3-Dependent E3 Ubiquitin Ligases.

Pinkas DM, Sanvitale CE, Bufton JC, Sorrell FJ, Solcan N, Chalk R, Doutch J, Bullock AN

Biochem. J.. doi: 10.1042/BCJ20170527

Publication date: September 28, 2017

PMID: 28963344

Corrigendum: Alternative splicing promotes tumour aggressiveness and drug resistance in African American prostate cancer.

Wang BD, Ceniccola K, Hwang S, Andrawis R, Horvath A, Freedman JA, Olender J, Knapp S, Ching T, Garmire L, Patel V, Garcia-Blanco MA, Patierno SR, Lee NH

Nat Commun. 8:16161. doi: 10.1038/ncomms16161

Publication date: September 27, 2017

PMID: 28952599

Crystal structure of the WD40 domain of human PRPF19.

Zhang Y, Li Y, Liang X, Zhu Z, Sun H, He H, Min J, Liao S, Liu Y

Biochem. Biophys. Res. Commun.. doi: 10.1016/j.bbrc.2017.09.145

Publication date: September 26, 2017

PMID: 28962858

Inhibition of calcium dependent protein kinase 1 (CDPK1) by pyrazolopyrimidine analogs decreases establishment and reoccurrence of central nervous system disease by Toxoplasma gondii.

Rutaganira FU, Barks J, Dhason MS, Wang Q, Lopez MS, Long S, Radke JB, Jones NG, Maddirala AR, Janetka JW, El Bakkouri M, Hui R, Shokat KM, Sibley LD

J. Med. Chem.. doi: 10.1021/acs.jmedchem.7b01192

Publication date: September 21, 2017

PMID: 28933846

Asymmetric mechanosensitivity in a eukaryotic ion channel.

Clausen MV, Jarerattanachat V, Carpenter EP, Sansom MSP, Tucker SJ

Proc. Natl. Acad. Sci. U.S.A.. doi: 10.1073/pnas.1708990114

Publication date: September 18, 2017

PMID: 28923939

Structural basis for the potent and selective binding of LDN-212854 to the BMP receptor kinase ALK2.

Williams E, Bullock AN

Bone. doi: 10.1016/j.bone.2017.09.004

Publication date: September 12, 2017

PMID: 28918311

Increased 15-PGDH expression leads to dysregulated resolution responses in stromal cells from patients with chronic tendinopathy.

Dakin SG, Ly L, Colas RA, Oppermann U, Wheway K, Watkins B, Dalli J, Carr AJ

Sci Rep. 7(1):11009. doi: 10.1038/s41598-017-11188-y

Publication date: September 8, 2017

PMID: 28887458

ASCL1 Reorganizes Chromatin to Direct Neuronal Fate and Suppress Tumorigenicity of Glioblastoma Stem Cells.

Park NI, Guilhamon P, Desai K, McAdam RF, Langille E, O'Connor M, Lan X, Whetstone H, Coutinho FJ, Vanner RJ, Ling E, Prinos P, Lee L, Selvadurai H, Atwal G, Kushida M, Clarke ID, Voisin V, Cusimano MD, Bernstein M, Das S, Bader G, Arrowsmith CH, Angers S, Huang X, Lupien M, Dirks PB

Cell Stem Cell. 21(3):411. doi: 10.1016/j.stem.2017.08.008

Publication date: September 7, 2017

PMID: 28886368

RAC1 Missense Mutations in Developmental Disorders with Diverse Phenotypes.

Reijnders MRF, Ansor NM, Kousi M, Yue WW, Tan PL, Clarkson K, Clayton-Smith J, Corning K, Jones JR, Lam WWK, Mancini GMS, Marcelis C, Mohammed S, Pfundt R, Roifman M, Cohn R, Chitayat D, Millard TH, Katsanis N, Brunner HG, Banka S

Am. J. Hum. Genet.. 101(3):466-477. doi: 10.1016/j.ajhg.2017.08.007

Publication date: September 7, 2017

PMID: 28886345

Novel patient missense mutations in the HSD17B10 gene affect dehydrogenase and mitochondrial tRNA modification functions of the encoded protein.

Oerum S, Roovers M, Leichsenring M, Acquaviva-Bourdain C, Beermann F, Gemperle-Britschgi C, Fouilhoux A, Korwitz-Reichelt A, Bailey HJ, Droogmans L, Oppermann U, Sass JO, Yue WW

Biochim. Biophys. Acta. doi: 10.1016/j.bbadis.2017.09.002

Publication date: September 6, 2017

PMID: 28888424

A potent series targeting the malarial cGMP-dependent protein kinase clears infection and blocks transmission.

Baker DA, Stewart LB, Large JM, Bowyer PW, Ansell KH, Jiménez-Díaz MB, El Bakkouri M, Birchall K, Dechering KJ, Bouloc NS, Coombs PJ, Whalley D, Harding DJ, Smiljanic-Hurley E, Wheldon MC, Walker EM, Dessens JT, Lafuente MJ, Sanz LM, Gamo FJ, Ferrer SB, Hui R, Bousema T, Angulo-Barturén I, Merritt AT, Croft SL, Gutteridge WE, Kettleborough CA, Osborne SA

Nat Commun. 8(1):430. doi: 10.1038/s41467-017-00572-x

Publication date: September 5, 2017

PMID: 28874661

First critical repressive H3K27me3 marks in embryonic stem cells identified using designed protein inhibitor.

Moody JD, Levy S, Mathieu J, Xing Y, Kim W, Dong C, Tempel W, Robitaille AM, Dang LT, Ferreccio A, Detraux D, Sidhu S, Zhu L, Carter L, Xu C, Valensisi C, Wang Y, Hawkins RD, Min J, Moon RT, Orkin SH, Baker D, Ruohola-Baker H

Proc. Natl. Acad. Sci. U.S.A.. doi: 10.1073/pnas.1706907114

Publication date: September 1, 2017

PMID: 28864533

Fate mapping of human glioblastoma reveals an invariant stem cell hierarchy.

Lan X, Jörg DJ, Cavalli FMG, Richards LM, Nguyen LV, Vanner RJ, Guilhamon P, Lee L, Kushida MM, Pellacani D, Park NI, Coutinho FJ, Whetstone H, Selvadurai HJ, Che C, Luu B, Carles A, Moksa M, Rastegar N, Head R, Dolma S, Prinos P, Cusimano MD, Das S, Bernstein M, Arrowsmith CH, Mungall AJ, Moore RA, Ma Y, Gallo M, Lupien M, Pugh TJ, Taylor MD, Hirst M, Eaves CJ, Simons BD, Dirks PB

Nature. doi: 10.1038/nature23666

Publication date: August 30, 2017

PMID: 28854171

Role of remodeling and spacing factor 1 in histone H2A ubiquitination-mediated gene silencing.

Zhang Z, Jones AE, Wu W, Kim J, Kang Y, Bi X, Gu Y, Popov IK, Renfrow MB, Vassylyeva MN, Vassylyev DG, Giles KE, Chen D, Kumar A, Fan Y, Tong Y, Liu CF, An W, Chang C, Luo J, Chow LT, Wang H

Proc. Natl. Acad. Sci. U.S.A.. doi: 10.1073/pnas.1711158114

Publication date: August 30, 2017

PMID: 28855339

Selective targeting of Bromodomains of the Bromodomain-PHD Fingers family impairs osteoclast differentiation.

Meier JC, Tallant C, Fedorov O, Witwicka H, Hwang SY, van Stiphout RG, Lambert JP, Rogers C, Yapp C, Gerstenberger BS, Fedele V, Savitsky P, Heidenreich D, Daniels DL, Owen DR, Fish PV, Igoe NM, Bayle ED, Haendler B, Oppermann UCT, Buffa F, Brennan PE, Müller S, Gingras AC, Odgren PR, Birnbaum MJ, Knapp S

ACS Chem. Biol.. doi: 10.1021/acschembio.7b00481

Publication date: August 29, 2017

PMID: 28849908

TFG facilitates outer coat disassembly on COPII transport carriers to promote tethering and fusion with ER-Golgi intermediate compartments.

Hanna MG, Block S, Frankel EB, Hou F, Johnson A, Yuan L, Knight G, Moresco JJ, Yates JR, Ashton R, Schekman R, Tong Y, Audhya A

Proc. Natl. Acad. Sci. U.S.A.. doi: 10.1073/pnas.1709120114

Publication date: August 29, 2017

PMID: 28851831

Comprehensive Analysis of the Human SH3 Domain Family Reveals a Wide Variety of Non-canonical Specificities.

Teyra J, Huang H, Jain S, Guan X, Dong A, Liu Y, Tempel W, Min J, Tong Y, Kim PM, Bader GD, Sidhu SS

Structure. doi: 10.1016/j.str.2017.07.017

Publication date: August 28, 2017

PMID: 28890361

Tudor-domain protein PHF20L1 reads lysine methylated retinoblastoma tumour suppressor protein.

Carr SM, Munro S, Sagum CA, Fedorov O, Bedford MT, La Thangue NB

Cell Death Differ.. doi: 10.1038/cdd.2017.135

Publication date: August 25, 2017

PMID: 28841214

A novel image-based high throughput screening assay discovers therapeutic candidates for adult polyglucosan body disease.

Solemsky LJ, Khazanov N, Senderowitz H, Wang P, Minassian BA, Ferreira IM, Yue WW, Lossos A, Weil M, Kakhlon O

Biochem. J.. doi: 10.1042/BCJ20170469

Publication date: August 21, 2017

PMID: 28827282

Studies on the Interaction of the Histone Demethylase KDM5B with Tricarboxylic Acid Cycle Intermediates.

Tarhonskaya H, Nowak RP, Johansson C, Szykowska A, Tumber A, Hancock RL, Lang P, Flashman E, Oppermann U, Schofield CJ, Kawamura A

J. Mol. Biol.. doi: 10.1016/j.jmb.2017.08.007

Publication date: August 18, 2017

PMID: 28827149

Characterization of a highly selective inhibitor of the Aurora kinases.

Ferguson FM, Doctor ZM, Chaikuad A, Sim T, Kim ND, Knapp S, Gray NS

Bioorg. Med. Chem. Lett.. doi: 10.1016/j.bmcl.2017.08.016

Publication date: August 10, 2017

PMID: 28818446

A statistical analysis on the performance of MMPBSA versus absolute binding free energy calculations: bromodomains as a case study.

Aldeghi M, Bodkin MJ, Knapp S, Biggin PC

J Chem Inf Model. doi: 10.1021/acs.jcim.7b00347

Publication date: August 8, 2017

PMID: 28786670

Structural characterization of human Vaccinia-Related Kinases (VRK) bound to small-molecule inhibitors identifies different P-loop conformations.

Couñago RM, Allerston CK, Savitsky P, Azevedo H, Godoi PH, Wells CI, Mascarello A, de Souza Gama FH, Massirer KB, Zuercher WJ, Guimarães CRW, Gileadi O

Sci Rep. 7(1):7501. doi: 10.1038/s41598-017-07755-y

Publication date: August 8, 2017

PMID: 28790404

Progress towards a public chemogenomic set for protein kinases and a call for contributions.

Drewry DH, Wells CI, Andrews DM, Angell R, Al-Ali H, Axtman AD, Capuzzi SJ, Elkins JM, Ettmayer P, Frederiksen M, Gileadi O, Gray N, Hooper A, Knapp S, Laufer S, Luecking U, Michaelides M, Müller S, Muratov E, Denny RA, Saikatendu KS, Treiber DK, Zuercher WJ, Willson TM

PLoS ONE. 12(8):e0181585. doi: 10.1371/journal.pone.0181585

Publication date: August 3, 2017

PMID: 28767711

(19) F NMR isotropic chemical shift for efficient screening of fluorinated fragments which are racemates and/or display multiple conformers.

Dalvit C, Knapp S

Magn Reson Chem. doi: 10.1002/mrc.4640

Publication date: August 1, 2017

PMID: 28762528

IDUA mutational profile and genotype-phenotype relationships in UK patients with Mucopolysaccharidosis I.

Ghosh A, Mercer J, Mackinnon S, Yue WW, Church H, Beesley CE, Broomfield A, Jones SA, Tylee K

Hum. Mutat.. doi: 10.1002/humu.23301

Publication date: July 28, 2017

PMID: 28752568

BRD3 and BRD4 BET Bromodomain Proteins Differentially Regulate Skeletal Myogenesis.

Roberts TC, Etxaniz U, Dall'Agnese A, Wu SY, Chiang CM, Brennan PE, Wood MJA, Puri PL

Sci Rep. 7(1):6153. doi: 10.1038/s41598-017-06483-7

Publication date: July 21, 2017

PMID: 28733670

Design of a chemical probe for the Bromodomain and Plant Homeodomain Finger-containing (BRPF) family of proteins.

Igoe N, Bayle ED, Tallant C, Fedorov O, Meier JC, Savitsky P, Rogers C, Morias Y, Scholze S, Boyd H, Cunoosamy D, Andrews DM, Cheasty A, Brennan PE, Müller S, Knapp S, Fish PV

J. Med. Chem.. doi: 10.1021/acs.jmedchem.7b00611

Publication date: July 17, 2017

PMID: 28714688

Global analysis of protein folding using massively parallel design, synthesis, and testing.

Rocklin GJ, Chidyausiku TM, Goreshnik I, Ford A, Houliston S, Lemak A, Carter L, Ravichandran R, Mulligan VK, Chevalier A, Arrowsmith CH, Baker D

Science. 357(6347):168-175. doi: 10.1126/science.aan0693

Publication date: July 14, 2017

PMID: 28706065

NEK1 kinase domain structure and its dynamic protein interactome after exposure to Cisplatin.

Melo-Hanchuk TD, Slepicka PF, Meirelles GV, Basei FL, Lovato DV, Granato DC, Pauletti BA, Domingues RR, Leme AFP, Pelegrini AL, Lenz G, Knapp S, Elkins JM, Kobarg J

Sci Rep. 7(1):5445. doi: 10.1038/s41598-017-05325-w

Publication date: July 14, 2017

PMID: 28710492

ASCL1 Reorganizes Chromatin to Direct Neuronal Fate and Suppress Tumorigenicity of Glioblastoma Stem Cells.

Park NI, Guilhamon P, Desai K, McAdam RF, Langille E, O'Connor M, Lan X, Whetstone H, Coutinho FJ, Vanner RJ, Ling E, Prinos P, Lee L, Selvadurai H, Atwal G, Kushida M, Clarke ID, Voisin V, Cusimano MD, Bernstein M, Das S, Bader G, Arrowsmith CH, Angers S, Huang X, Lupien M, Dirks PB

Cell Stem Cell. doi: 10.1016/j.stem.2017.06.004

Publication date: July 11, 2017

PMID: 28712938

Alternative splicing promotes tumour aggressiveness and drug resistance in African American prostate cancer.

Wang BD, Ceniccola K, Hwang S, Andrawis R, Horvath A, Freedman JA, Olender J, Knapp S, Ching T, Garmire L, Patel V, Garcia-Blanco MA, Patierno SR, Lee NH

Nat Commun. 8:15921. doi: 10.1038/ncomms15921

Publication date: June 30, 2017

PMID: 28665395

Structure-activity relationship studies of G9a-like protein (GLP) inhibitors.

Xiong Y, Li F, Babault N, Wu H, Dong A, Zeng H, Chen X, Arrowsmith CH, Brown PJ, Liu J, Vedadi M, Jin J

Bioorg. Med. Chem.. doi: 10.1016/j.bmc.2017.06.021

Publication date: June 19, 2017

PMID: 28662962

Readers, writers and erasers of N(6)-methylated adenosine modification.

Wu B, Li L, Huang Y, Ma J, Min J

Curr. Opin. Struct. Biol.. 47:67-76. doi: 10.1016/j.sbi.2017.05.011

Publication date: June 15, 2017

PMID: 28624569

Structural Characterization of Maize SIRK1 Kinase Domain Reveals an Unusual Architecture of the Activation Segment.

Aquino B, Couñago RM, Verza N, Ferreira LM, Massirer KB, Gileadi O, Arruda P

Front Plant Sci. 8:852. doi: 10.3389/fpls.2017.00852

Publication date: June 13, 2017

PMID: 28603531

Structures of PGAM5 Provide Insight into Active Site Plasticity and Multimeric Assembly.

Chaikuad A, Filippakopoulos P, Marcsisin SR, Picaud S, Schröder M, Sekine S, Ichijo H, Engen JR, Takeda K, Knapp S

Structure. doi: 10.1016/j.str.2017.05.020

Publication date: June 10, 2017

PMID: 28648608

Generation and validation of intracellular ubiquitin variant inhibitors for USP7 and USP10.

Zhang W, Sartori MA, Makhnevych T, Federowicz KE, Dong X, Liu L, Nim S, Dong A, Yang J, Li Y, Haddad D, Ernst A, Heerding D, Tong Y, Moffat J, Sidhu SS

J. Mol. Biol.. doi: 10.1016/j.jmb.2017.05.025

Publication date: June 3, 2017

PMID: 28587923