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)

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
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9H5I1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NM4 (Subject of Investigation/LOI) Query on NM4 Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain C [auth A]	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		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain E [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] J [auth B] 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		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A]	H [auth A], M [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain H [auth A] Focus chain M [auth B] Interactions & Density Focus chain H [auth A] Focus chain M [auth B]

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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-05-29

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

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