4FMU

Crystal structure of Methyltransferase domain of human SET domain-containing protein 2 Compound: Pr-SNF

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

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:  
    4H12, 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 individual PKMTs can be facilitated by target-specific PKMT inhibitors ...

    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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase SETD2A278Homo sapiensMutation(s): 0 
Gene Names: SETD2, HIF1, HYPB, KIAA1732, KMT3A, SET2, HSPC069
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.359 (UniProt), 2.1.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYW2 (Homo sapiens)
Explore Q9BYW2 
Go to UniProtKB:  Q9BYW2
PHAROS:  Q9BYW2
GTEx:  ENSG00000181555
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0UM
Query on 0UM
Download Ideal Coordinates CCD File 
 E [auth A](2S,5S)-2-amino-6-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]-5-(propylamino)hexanoic acid
C18 H29 N7 O5
ZDIZXAAADLAUDS-GTAFEMJLSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
 B [auth A], C [auth A], D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
UNX
Query on UNX
Download Ideal Coordinates CCD File 
F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , L [auth A] , M [auth A] , 
F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  N [auth A],  O [auth A],  P [auth A],  Q [auth A],  R [auth A]
UNKNOWN ATOM OR ION
X
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0UMKd :  360   nM  PDBBind
0UMKd:  360   nM  Binding MOAD
0UMIC50:  800   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.547α = 90
b = 77.277β = 90
c = 78.864γ = 90
Software Package:
Software NamePurpose
JBlulce-EPICSdata collection
MOLREPphasing
BUSTERrefinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-05
    Type: Initial release
  • Version 1.1: 2012-10-24
    Changes: Database references
  • Version 1.2: 2012-11-14
    Changes: Database references