4E47

SET7/9 in complex with inhibitor (R)-(3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl)-1,2,3,4-tetrahydroisoquinoline-6- sulfonamide and S-adenosylmethionine

PDB DOI: https://doi.org/10.2210/pdb4E47/pdb

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

Deposited: 2012-03-12 Released: 2012-03-28
Deposition Author(s): Walker, J.R., Ouyang, H., Dong, A., Fish, P., Cook, A., Barsyte, D., Vedadi, M., Tatlock, J., Owen, D., Bunnage, M., Bountra, C., Weigelt, J., Edwards, A.M., Arrowsmith, C.H., Brown, P.J., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.201
R-Value Work: 0.160
R-Value Observed: 0.162

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Setd7 in Complex with Inhibitor and SAM

Walker, J.R., Ouyang, H., Dong, A., Fish, P., Cook, A., Barsyte, D., Vedadi, M., Tatlock, J., Owen, D., Bunnage, M., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Brown, P.J., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 122.26 kDa
Atom Count: 8,934
Modelled Residue Count: 986
Deposited Residue Count: 1,056
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 SETD7	A, B, C, D	264	Homo sapiens	Mutation(s): 0 Gene Names: SETD7, KIAA1717, KMT7, SET7, SET9 EC: 2.1.1.43 (PDB Primary Data), 2.1.1.364 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WTS6 (Homo sapiens) Explore Q8WTS6 Go to UniProtKB: Q8WTS6
PHAROS: Q8WTS6 GTEx: ENSG00000145391
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8WTS6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0N6 Query on 0N6 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D]	F [auth A], J [auth B], L [auth C], N [auth D]	(R)-(3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl)-1,2,3,4-tetrahydroisoquinoline-6-sulfonamide C₂₃ H₂₆ N₄ O₃ S WWKTZMSNGFQJAG-JOCHJYFZSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D]
SAM Query on SAM Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	E [auth A], I [auth B], K [auth C], M [auth D]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.201
R-Value Work: 0.160
R-Value Observed: 0.162
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.343	α = 90
b = 133.799	β = 90
c = 136.865	γ = 90

Software Package:

Software Name	Purpose
JBluIce-EPICS	data collection
PHASER	phasing
BUSTER	refinement
Coot	model building
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-03-28

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2012-03-28
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description