Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32.58 kDa 
• Atom Count: 1957 
• Modelled Residue Count: 235 
• Deposited Residue Count: 278 
• Unique protein chains: 1

4FMU

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

• PDB DOI: 10.2210/pdb4FMU/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-06-18 Released: 2012-09-05 
• Deposition Author(s): Dong, A., Zeng, H., Ibanez, G., Zheng, W., Tempel, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Brown, P.J., Min, J., Luo, M., Wu, H., Structural Genomics Consortium (SGC)

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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 

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

• PubMed: 23043551 
• DOI: 10.1021/ja307060p
• Primary Citation of Related Structures:  
  4FMU, 4H12


• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase SETD2	A	278	Homo sapiens	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0UM	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
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
UNX	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

Binding Affinity Annotations
ID	Source	Binding Affinity
0UM	Binding MOAD:  4FMU	Kd: 360 (nM) from 1 assay(s)
	PDBBind:  4FMU	Kd: 360 (nM) from 1 assay(s)
	BindingDB:  4FMU	IC50: 800 (nM) from 1 assay(s)

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 = 51.547	α = 90
b = 77.277	β = 90
c = 78.864	γ = 90

Software Package:

Software Name	Purpose
JBlulce-EPICS	data collection
MOLREP	phasing
BUSTER	refinement
Coot	model building
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-06-18 
• Released Date: 2012-09-05 
Deposition Author(s): Dong, A., Zeng, H., Ibanez, G., Zheng, W., Tempel, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Brown, P.J., Min, J., Luo, M., Wu, H., Structural Genomics Consortium (SGC)

Revision History  

• 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