4H12

The crystal structure of methyltransferase domain of human SET domain-containing protein 2 in complex with S-adenosyl-L-homocysteine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Sinefungin Derivatives as Inhibitors and Structure Probes of Protein Lysine Methyltransferase SETD2.

Zheng, W.Ibanez, G.Wu, H.Blum, G.Zeng, H.Dong, A.Li, F.Hajian, T.Allali-Hassani, A.Amaya, M.F.Siarheyeva, A.Yu, W.Brown, P.J.Schapira, M.Vedadi, M.Min, J.Luo, M.

(2012) J.Am.Chem.Soc. 134: 18004-18014

  • DOI: 10.1021/ja307060p
  • Primary Citation of Related Structures:  4FMU

  • PubMed Abstract: 
  • Epigenetic regulation is involved in numerous physiological and pathogenic processes. Among the key regulators that orchestrate epigenetic signaling are over 50 human protein lysine methyltransferases (PKMTs). Interrogation of the functions of indivi ...

    Epigenetic regulation is involved in numerous physiological and pathogenic processes. Among the key regulators that orchestrate epigenetic signaling are over 50 human protein lysine methyltransferases (PKMTs). Interrogation of the functions of individual PKMTs can be facilitated by target-specific PKMT inhibitors. Given the emerging need for such small molecules, we envisioned an approach to identify target-specific methyltransferase inhibitors by screening privileged small-molecule scaffolds against diverse methyltransferases. In this work, we demonstrated the feasibility of such an approach by identifying the inhibitors of SETD2. N-propyl sinefungin (Pr-SNF) was shown to interact preferentially with SETD2 by matching the distinct transition-state features of SETD2's catalytically active conformer. With Pr-SNF as a structure probe, we further revealed the dual roles of SETD2's post-SET loop in regulating substrate access through a distinct topological reconfiguration. Privileged sinefungin scaffolds are expected to have broad use as structure and chemical probes of methyltransferases.


    Organizational Affiliation

    Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase SETD2
A
278Homo sapiensGene Names: SETD2 (HIF1, HYPB, KIAA1732, KMT3A, SET2)
EC: 2.1.1.43
Find proteins for Q9BYW2 (Homo sapiens)
Go to Gene View: SETD2
Go to UniProtKB:  Q9BYW2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.293α = 90.00
b = 76.663β = 90.00
c = 78.093γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data scaling
HKL-3000data collection
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2012-10-24
    Type: Database references
  • Version 1.2: 2012-11-14
    Type: Database references