5KCH | pdb_00005kch

SETDB1 in complex with an early stage, low affinity fragment candidate modelled at reduced occupancy into weak electron density

PDB DOI: https://doi.org/10.2210/pdb5KCH/pdb

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

Deposited: 2016-06-06 Released: 2016-07-27
Deposition Author(s): Tempel, W., Harding, R.J., Mader, P., Dobrovetsky, E., Walker, J.R., Brown, P.J., Schapira, M., Collins, P., Pearce, N., Brandao-Neto, J., Douangamath, A., von Delft, F., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Santhakumar, V., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.258 (Depositor), 0.263 (DCC)
R-Value Work:
0.215 (Depositor), 0.223 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

SETDB1 in complex with an early stage, low affinity fragment candidate modelled at reduced occupancy

Tempel, W., Harding, R.J., Mader, P., Dobrovetsky, E., Walker, J.R., Brown, P.J., Schapira, M., Arrowsmith, C.H., Edwards, A.M., Santhakumar, S., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 42.94 kDa
Atom Count: 1,910
Modeled Residue Count: 212
Deposited Residue Count: 225
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase SETDB1	A	225	Homo sapiens	Mutation(s): 0 Gene Names: SETDB1, KIAA0067, KMT1E EC: 2.1.1.43 (PDB Primary Data), 2.1.1.366 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q15047 (Homo sapiens) Explore Q15047 Go to UniProtKB: Q15047
PHAROS: Q15047 GTEx: ENSG00000143379
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15047
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6RN Query on 6RN Download:Ideal Coordinates CCD File SDF format, chain CB [auth A] MOL2 format, chain CB [auth A] mmCIF format, chain CB [auth A]	CB [auth A]	4-methoxy-N-[(pyridin-2-yl)methyl]aniline C₁₃ H₁₄ N₂ O VZYUNDIQWDHYLW-UHFFFAOYSA-N		Interactions Focus chain CB [auth A] Interactions & Density Focus chain CB [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain BB [auth A] SDF format, chain AB [auth A] MOL2 format, chain BB [auth A] MOL2 format, chain AB [auth A] mmCIF format, chain BB [auth A] mmCIF format, chain AB [auth A]	AB [auth A], BB [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AB [auth A] Focus chain BB [auth A] Interactions & Density Focus chain AB [auth A] Focus chain BB [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain ZA [auth A] MOL2 format, chain ZA [auth A] mmCIF format, chain ZA [auth A]	ZA [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain ZA [auth A] Interactions & Density Focus chain ZA [auth A]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain B [auth A] SDF format, chain BA [auth A] SDF format, chain C [auth A] SDF format, chain CA [auth A] SDF format, chain D [auth A] SDF format, chain DA [auth A] SDF format, chain E [auth A] SDF format, chain EA [auth A] SDF format, chain F [auth A] SDF format, chain FA [auth A] SDF format, chain G [auth A] SDF format, chain GA [auth A] SDF format, chain H [auth A] SDF format, chain HA [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth A] SDF format, chain NA [auth A] SDF format, chain P [auth A] SDF format, chain QA [auth A] SDF format, chain R [auth A] SDF format, chain RA [auth A] SDF format, chain S [auth A] SDF format, chain SA [auth A] SDF format, chain T [auth A] SDF format, chain TA [auth A] SDF format, chain U [auth A] SDF format, chain UA [auth A] SDF format, chain VA [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain XA [auth A] SDF format, chain Y [auth A] SDF format, chain YA [auth A] SDF format, chain Z [auth A] SDF format, chain WA [auth A] SDF format, chain V [auth A] SDF format, chain Q [auth A] SDF format, chain PA [auth A] SDF format, chain OA [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain B [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain C [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain D [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain P [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain VA [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain WA [auth A] MOL2 format, chain V [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain B [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain C [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain D [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain P [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth A] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth A] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth A] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth A] mmCIF format, chain VA [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain WA [auth A] mmCIF format, chain V [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain OA [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A]	AA [auth A] B [auth A] BA [auth A] C [auth A] CA [auth A] AA [auth A], B [auth A], BA [auth A], C [auth A], CA [auth A], D [auth A], DA [auth A], E [auth A], EA [auth A], F [auth A], FA [auth A], G [auth A], GA [auth A], H [auth A], HA [auth A], I [auth A], IA [auth A], J [auth A], JA [auth A], K [auth A], KA [auth A], L [auth A], LA [auth A], M [auth A], MA [auth A], N [auth A], NA [auth A], O [auth A], OA [auth A], P [auth A], PA [auth A], Q [auth A], QA [auth A], R [auth A], RA [auth A], S [auth A], SA [auth A], T [auth A], TA [auth A], U [auth A], UA [auth A], V [auth A], VA [auth A], W [auth A], WA [auth A], X [auth A], XA [auth A], Y [auth A], YA [auth A], Z [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain AA [auth A] Focus chain B [auth A] Focus chain BA [auth A] Focus chain C [auth A] Focus chain CA [auth A] Focus chain D [auth A] Focus chain DA [auth A] Focus chain E [auth A] Focus chain EA [auth A] Focus chain F [auth A] Focus chain FA [auth A] Focus chain G [auth A] Focus chain GA [auth A] Focus chain H [auth A] Focus chain HA [auth A] Focus chain I [auth A] Focus chain IA [auth A] Focus chain J [auth A] Focus chain JA [auth A] Focus chain K [auth A] Focus chain KA [auth A] Focus chain L [auth A] Focus chain LA [auth A] Focus chain M [auth A] Focus chain MA [auth A] Focus chain N [auth A] Focus chain NA [auth A] Focus chain O [auth A] Focus chain OA [auth A] Focus chain P [auth A] Focus chain PA [auth A] Focus chain Q [auth A] Focus chain QA [auth A] Focus chain R [auth A] Focus chain RA [auth A] Focus chain S [auth A] Focus chain SA [auth A] Focus chain T [auth A] Focus chain TA [auth A] Focus chain U [auth A] Focus chain UA [auth A] Focus chain V [auth A] Focus chain VA [auth A] Focus chain W [auth A] Focus chain WA [auth A] Focus chain X [auth A] Focus chain XA [auth A] Focus chain Y [auth A] Focus chain YA [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain B [auth A] Focus chain BA [auth A] Focus chain C [auth A] Focus chain CA [auth A] Focus chain D [auth A] Focus chain DA [auth A] Focus chain E [auth A] Focus chain EA [auth A] Focus chain F [auth A] Focus chain FA [auth A] Focus chain G [auth A] Focus chain GA [auth A] Focus chain H [auth A] Focus chain HA [auth A] Focus chain I [auth A] Focus chain IA [auth A] Focus chain J [auth A] Focus chain JA [auth A] Focus chain K [auth A] Focus chain KA [auth A] Focus chain L [auth A] Focus chain LA [auth A] Focus chain M [auth A] Focus chain MA [auth A] Focus chain N [auth A] Focus chain NA [auth A] Focus chain O [auth A] Focus chain OA [auth A] Focus chain P [auth A] Focus chain PA [auth A] Focus chain Q [auth A] Focus chain QA [auth A] Focus chain R [auth A] Focus chain RA [auth A] Focus chain S [auth A] Focus chain SA [auth A] Focus chain T [auth A] Focus chain TA [auth A] Focus chain U [auth A] Focus chain UA [auth A] Focus chain V [auth A] Focus chain VA [auth A] Focus chain W [auth A] Focus chain WA [auth A] Focus chain X [auth A] Focus chain XA [auth A] Focus chain Y [auth A] Focus chain YA [auth A] Focus chain Z [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.258 (Depositor), 0.263 (DCC)
R-Value Work: 0.215 (Depositor), 0.223 (DCC)
R-Value Observed: 0.217 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.967	α = 90
b = 63.607	β = 90
c = 70.457	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-07-27

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2016-07-27
Type: Initial release
Version 1.1: 2017-01-25
Changes: Structure summary
Version 2.0: 2019-02-20
Changes: Advisory, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-09-27
Changes: Data collection, Database references, Refinement description