6P0R | pdb_00006p0r

Methyltransferase domain of human suppressor of variegation 3-9 homolog 2 (SUV39H2) in complex with OTS186935 inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6P0R/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-05-17 Released: 2019-05-29 
• Deposition Author(s): Halabelian, L., Dong, A., Zeng, H., Loppnau, P., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Brown, P.J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.267 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Methyltransferase domain of human suppressor of variegation 3-9 homolog 2 (SUV39H2) in complex with OTS186935 inhibitor

Halabelian, L., Dong, A., Zeng, H., Loppnau, P., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Brown, P.J., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 69.36 kDa 
• Atom Count: 3,777 
• Modeled Residue Count: 485 
• Deposited Residue Count: 598 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase SUV39H2	A, B	299	Homo sapiens	Mutation(s): 0  Gene Names: SUV39H2, KMT1B EC: 2.1.1.43 (PDB Primary Data), 2.1.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H5I1 (Homo sapiens) Explore Q9H5I1  Go to UniProtKB:  Q9H5I1
PHAROS:  Q9H5I1 GTEx:  ENSG00000152455

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NM4 (Subject of Investigation/LOI)	C [auth A], I [auth B]	(3S)-1-[2-(5-chloro-2,4-dimethoxyphenyl)imidazo[1,2-a]pyridin-7-yl]-N-[(pyridin-4-yl)methyl]pyrrolidin-3-amine C25 H26 Cl N5 O2 YDTCRGKEOJGNHD-SFHVURJKSA-N
ZN	D [auth A], E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
UNX	H [auth A], M [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.267 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.701	α = 90
b = 63.388	β = 113.17
c = 65.616	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-3000	data processing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-05-29 
Deposition Author(s): Halabelian, L., Dong, A., Zeng, H., Loppnau, P., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Brown, P.J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2019-05-29
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description