6CBX

Crystal structure of human SET and MYND Domain Containing protein 2 with MTF1497

PDB DOI: https://doi.org/10.2210/pdb6CBX/pdb

Classification: TRANSFERASE/INHIBITOR
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2018-02-05 Released: 2018-03-14
Deposition Author(s): ZENG, H., DONG, A., Hutchinson, A., Seitova, A., TATLOCK, J., KUMPF, R., OWEN, A., TAYLOR, A., Casimiro-Garcia, A., Bountra, C., Arrowsmith, C.H., Edwards, A.M., BROWN, P.J., WU, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.223
R-Value Work: 0.180
R-Value Observed: 0.181

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of human SET and MYND Domain Containing protein 2 with MTF1497

ZENG, H., DONG, A., Hutchinson, A., Seitova, A., TATLOCK, J., KUMPF, R., OWEN, A., TAYLOR, A., Casimiro-Garcia, A., Bountra, C., Arrowsmith, C.H., Edwards, A.M., BROWN, P.J., WU, H., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 101.47 kDa
Atom Count: 7,344
Modelled Residue Count: 861
Deposited Residue Count: 868
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-lysine methyltransferase SMYD2	A, B	434	Homo sapiens	Mutation(s): 0 Gene Names: SMYD2, KMT3C EC: 2.1.1 (PDB Primary Data), 2.1.1.43 (PDB Primary Data), 2.1.1.354 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRG4 (Homo sapiens) Explore Q9NRG4 Go to UniProtKB: Q9NRG4
PHAROS: Q9NRG4 GTEx: ENSG00000143499
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NRG4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EW1 Query on EW1 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain R [auth B] MOL2 format, chain F [auth A] MOL2 format, chain R [auth B] mmCIF format, chain F [auth A] mmCIF format, chain R [auth B]	F [auth A], R [auth B]	[3-(4-amino-6-methyl-1H-imidazo[4,5-c]pyridin-1-yl)azetidin-1-yl][1-({1-[(1R)-cyclohept-2-en-1-yl]piperidin-4-yl}methyl )-1H-pyrrol-3-yl]methanone C₂₈ H₃₇ N₇ O HQHAEFHJXLPTMM-QHCPKHFHSA-N		Interactions Focus chain F [auth A] Focus chain R [auth B] Interactions & Density Focus chain F [auth A] Focus chain R [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B]	C [auth A] D [auth A] E [auth A] O [auth B] P [auth B] C [auth A], D [auth A], E [auth A], O [auth B], P [auth B], Q [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	H [auth A], I [auth A], T [auth B], U [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain T [auth B] Focus chain U [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain S [auth B] MOL2 format, chain G [auth A] MOL2 format, chain S [auth B] mmCIF format, chain G [auth A] mmCIF format, chain S [auth B]	G [auth A], S [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain S [auth B] Interactions & Density Focus chain G [auth A] Focus chain S [auth B]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	J [auth A] K [auth A] L [auth A] M [auth A] N [auth A] J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.223
R-Value Work: 0.180
R-Value Observed: 0.181
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/m36cbx

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.02	α = 90
b = 117.031	β = 92.54
c = 64.444	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-03-14

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2018-03-14
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references, Derived calculations, Structure summary