5TEG

Crystal structure of hSETD8 in complex with histone H4K20 norleucine mutant peptide and S-Adenosylmethionine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Turning a Substrate Peptide into a Potent Inhibitor for the Histone Methyltransferase SETD8.

Judge, R.A.Zhu, H.Upadhyay, A.K.Bodelle, P.M.Hutchins, C.W.Torrent, M.Marin, V.L.Yu, W.Vedadi, M.Li, F.Brown, P.J.Pappano, W.N.Sun, C.Petros, A.M.

(2016) ACS Med Chem Lett 7: 1102-1106

  • DOI: 10.1021/acsmedchemlett.6b00303

  • PubMed Abstract: 
  • SETD8 is a histone H4-K20 methyltransferase that plays an essential role in the maintenance of genomic integrity during mitosis and in DNA damage repair, making it an intriguing target for cancer research. While some small molecule inhibitors for SET ...

    SETD8 is a histone H4-K20 methyltransferase that plays an essential role in the maintenance of genomic integrity during mitosis and in DNA damage repair, making it an intriguing target for cancer research. While some small molecule inhibitors for SETD8 have been reported, the structural binding modes for these inhibitors have not been revealed. Using the complex structure of the substrate peptide bound to SETD8 as a starting point, different natural and unnatural amino acid substitutions were tested, and a potent ( K i 50 nM, IC 50 0.33 μM) and selective norleucine containing peptide inhibitor has been obtained.


    Organizational Affiliation

    Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea. Electronic address: chahong@korea.ac.kr.,Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.,Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, BCC206, La Jolla, CA 92037, USA.,Ferrier Research Institute, Victoria University of Wellington, Wellington 6140, New Zealand.,Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, MA 21224, USA.,Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.,Dipartimento di Scienze della Terra , Università di Pisa , via Santa Maria 53 , 56126 Pisa , Italy.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.,Division of Bioconvergence Analysis, Korea Basic Science Institute, 162 Yeongudangiro Ochang, Cheongwongu, Cheongju, Chungbuk 28119, South Korea.,Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands. t.sharp@lumc.nl p.w.h.i.parren@lumc.nl p.gros@uu.nl.,Laboratory Molecular and Cellular Signaling, Department Cellular and Molecular Medicine, Campus Gasthuisberg O/N-I Bus 802, Herestraat 49 3000 Leuven, Belgium.,Genmab, Yalelaan 60, 3584 CM Utrecht, Netherlands.,Genmab, Yalelaan 60, 3584 CM Utrecht, Netherlands. t.sharp@lumc.nl p.w.h.i.parren@lumc.nl p.gros@uu.nl.,Department of Chemistry and Biochemistry, University of Lethbridge, Alberta T1K 3M4, Canada.,MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK. s.s.virdee@dundee.ac.uk.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1142, New Zealand.,Chemistry Department, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.,RNA Therapeutics Institute and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States.,Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA; NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA.,Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA.,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK. simonasm@mrc-lmb.cam.ac.uk.,Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA; NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA. Electronic address: qunliu@bnl.gov.,Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany.,Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK. radu@mrc-lmb.cam.ac.uk.,Materials and Structural Analysis, Thermo Fisher Scientific, Eindhoven, The Netherlands.,Institute of Fundamental Sciences and the Riddet Institute, Massey University, Palmerston North 4442, New Zealand.,Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China.,Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China.,NHC Key Laboratory of Cancer Proteomics & Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China. yonghenc@163.com.,Institute of Molecular Systems Biology and Department of Health Sciences and Technology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.,Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA mr@purdue.edu.,Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium.,Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK.,Institute for Genetics, University of Cologne, Cologne, Germany.,Dipartimento di Farmacia , Università di Pisa , Via Bonanno 6 , 56126 Pisa , Italy.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.,CEA, Institut des Sciences du Vivant Frédéric Joliot, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO) , Université Paris-Saclay , Gif-sur-Yvette 91190 , France.,SAXS/WAXS, Australian Synchrotron/ANSTO, 800 Blackburn Road, Clayton, VIC 3168, Australia.,Section of Electron Microscopy, Department of Molecular Cell Biology, Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, Netherlands.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China. shaofeng@nibs.ac.cn.,Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.,Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA. kwmiller@mgh.harvard.edu.,Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia.,Department of Biology, Molecular Basis of Disease Program, Department of Computer Science, and Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States.,Biomolecular Interaction Centre and School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8041, New Zealand emily.parker@vuw.ac.nz g.b.jameson@massey.ac.nz.,Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands.,Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.,Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.,Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium.,Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan.,NeCEN, Gorlaeus Laboratories, Leiden University, 2333 CC Leiden, Netherlands.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,MOH Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,National Institute of Biological Sciences, Beijing, China. shaofeng@nibs.ac.cn.,Institute for Advanced Biosciences, Keio University, 14-1 Baba-cho, Tsuruoka, Yamagata 997-0035, Japan.,National Institute of Biological Sciences, Beijing, China.,Centro de Química Estrutural, Instituto Superior Técnico , Universidade de Lisboa , Av. Rovisco Pais 1 , 1049-001 Lisboa , Portugal.,Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Synchrotron SOLEIL , L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette , France.,Laboratory of Biomolecular Research, Division of Biology and Chemistry , Paul Scherrer Institute , 5232 Villigen , Switzerland.,Instituto de Bionanotecnología del NOA, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Santiago del Estero, G4206XCP Santiago del Estero, Argentina.,Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany goerlich@mpibpc.mpg.de.,Structural Genomics Consortium, University of Toronto , 101 College Street, Toronto, ON M5G 1L7, Canada.,Shanghai Public Health Clinical Center and School of Basic Medical Sciences, and Key Laboratory of Medical Molecular Virology of MOE/MOH, Fudan University, Shanghai 200032, China.,Section of Electron Microscopy, Department of Molecular Cell Biology, Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, Netherlands. t.sharp@lumc.nl p.w.h.i.parren@lumc.nl p.gros@uu.nl.,Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, MA 21224, USA. Electronic address: lei.shi2@nih.gov.,Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK. radu@mrc-lmb.cam.ac.uk.,Biomolecular Interaction Centre and School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8041, New Zealand.,Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea.,Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, South Korea.,AbbVie Inc. , 1 North Waukegan Road, North Chicago, Illinois 60064, United States.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. shaofeng@nibs.ac.cn.,Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. nisimasu@bs.s.u-tokyo.ac.jp nureki@bs.s.u-tokyo.ac.jp.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,McGovern Institute for Brain Research, Cambridge, MA 02139, USA.,Beijing Mingde Zhengkang Technologies Co., Ltd., Beijing, China.,New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY 10027, USA.,Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, South Korea; Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea.,Department of Psychiatry, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA. Electronic address: mq2102@cumc.columbia.edu.,College of Animal Science and Technology, China Agricultural University, Beijing, China.,Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-lysine methyltransferase KMT5A
A, B
160Homo sapiensMutation(s): 1 
Gene Names: KMT5A (PRSET7, SET07, SET8, SETD8)
EC: 2.1.1.-
Find proteins for Q9NQR1 (Homo sapiens)
Go to Gene View: KMT5A
Go to UniProtKB:  Q9NQR1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4 mutant peptide with H4K20norleucine
D, E
8Homo sapiensMutation(s): 0 
Gene Names: HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4A, HIST2H4B, HIST4H4 (H4/A, H4FA, H4/I, H4FI, H4/G, H4FG, H4/B, H4FB, H4/J, H4FJ, H4/C, H4FC, H4/H, H4FH, H4/M, H4FM, H4/E, H4FE, H4/D, H4FD, H4/K, H4FK, H4/N, H4F2, H4FN, HIST2H4, H4/O, H4FO)
Find proteins for P62805 (Homo sapiens)
Go to UniProtKB:  P62805
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download SDF File 
Download CCD File 
A, B
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NLE
Query on NLE
D, E
L-PEPTIDE LINKINGC6 H13 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.189 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 44.310α = 114.73
b = 45.059β = 90.77
c = 52.649γ = 90.81
Software Package:
Software NamePurpose
MOLREPphasing
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTER-TNTrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2016-12-21
    Type: Database references
  • Version 1.2: 2018-04-25
    Type: Data collection, Database references