4JDS | pdb_00004jds

SETD7 in complex with inhibitor PF-5426 and S-adenosyl-methionine

PDB DOI: https://doi.org/10.2210/pdb4JDS/pdb

Classification: transferase/transferase inhibitor
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-02-25 Released: 2013-03-27
Deposition Author(s): Dong, A., Wu, H., Zeng, H., Park, H., El Bakkouri, M., Barsyte, D., Vedadi, M., Tatlock, J., Owen, D., Bunnage, M., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Brown, P.J., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.223 (Depositor), 0.228 (DCC)
R-Value Work:
0.199 (Depositor), 0.198 (DCC)
R-Value Observed:
0.199 (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

SETD7 in complex with inhibitor PF-5426 and S-adenosyl-methionine

Dong, A., Wu, H., Zeng, H., El Bakkouri, M., Barsyte, D., Vedadi, M., Tatlock, J., Owen, D., Bunnage, M., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Brown, P.J.

To be published.

Macromolecule Content

Total Structure Weight: 122.16 kDa
Atom Count: 8,940
Modeled Residue Count: 977
Deposited Residue Count: 1,056
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 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8WTS6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1L4 Query on 1L4 Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain QA [auth D] SDF format, chain FA [auth C] SDF format, chain F [auth A] MOL2 format, chain V [auth B] MOL2 format, chain QA [auth D] MOL2 format, chain FA [auth C] MOL2 format, chain F [auth A] mmCIF format, chain V [auth B] mmCIF format, chain QA [auth D] mmCIF format, chain FA [auth C] mmCIF format, chain F [auth A]	F [auth A], FA [auth C], QA [auth D], V [auth B]	N-[(2R)-3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl]-8-fluoro-1,2,3,4-tetrahydroisoquinoline-6-sulfonamide C₂₃ H₂₅ F N₄ O₃ S HMBXWXQQVHJMOO-JOCHJYFZSA-N		Interactions Focus chain F [auth A] Focus chain FA [auth C] Focus chain QA [auth D] Focus chain V [auth B] Interactions & Density Focus chain F [auth A] Focus chain FA [auth C] Focus chain QA [auth D] Focus chain V [auth B]
SAM Query on SAM Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain PA [auth D] SDF format, chain EA [auth C] SDF format, chain E [auth A] MOL2 format, chain U [auth B] MOL2 format, chain PA [auth D] MOL2 format, chain EA [auth C] MOL2 format, chain E [auth A] mmCIF format, chain U [auth B] mmCIF format, chain PA [auth D] mmCIF format, chain EA [auth C] mmCIF format, chain E [auth A]	E [auth A], EA [auth C], PA [auth D], U [auth B]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain E [auth A] Focus chain EA [auth C] Focus chain PA [auth D] Focus chain U [auth B] Interactions & Density Focus chain E [auth A] Focus chain EA [auth C] Focus chain PA [auth D] Focus chain U [auth B]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain WA [auth D] SDF format, chain W [auth B] SDF format, chain VA [auth D] SDF format, chain UA [auth D] SDF format, chain TA [auth D] SDF format, chain T [auth A] SDF format, chain SA [auth D] SDF format, chain S [auth A] SDF format, chain RA [auth D] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain OA [auth C] SDF format, chain O [auth A] SDF format, chain NA [auth C] SDF format, chain N [auth A] SDF format, chain MA [auth C] SDF format, chain M [auth A] SDF format, chain LA [auth C] SDF format, chain L [auth A] SDF format, chain KA [auth C] SDF format, chain K [auth A] SDF format, chain JA [auth C] SDF format, chain J [auth A] SDF format, chain IA [auth C] SDF format, chain I [auth A] SDF format, chain HA [auth C] SDF format, chain H [auth A] SDF format, chain GA [auth C] SDF format, chain G [auth A] SDF format, chain DA [auth B] SDF format, chain CA [auth B] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain VA [auth D] MOL2 format, chain UA [auth D] MOL2 format, chain TA [auth D] MOL2 format, chain T [auth A] MOL2 format, chain SA [auth D] MOL2 format, chain S [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain WA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain VA [auth D] mmCIF format, chain UA [auth D] mmCIF format, chain TA [auth D] mmCIF format, chain T [auth A] mmCIF format, chain SA [auth D] mmCIF format, chain S [auth A] mmCIF format, chain RA [auth D] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] G [auth A] AA [auth B], BA [auth B], CA [auth B], DA [auth B], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], Q [auth A], R [auth A], RA [auth D], S [auth A], SA [auth D], T [auth A], TA [auth D], UA [auth D], VA [auth D], W [auth B], WA [auth D], X [auth B], Y [auth B], Z [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain RA [auth D] Focus chain S [auth A] Focus chain SA [auth D] Focus chain T [auth A] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain RA [auth D] Focus chain S [auth A] Focus chain SA [auth D] Focus chain T [auth A] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] 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: 1.70 Å
R-Value Free: 0.223 (Depositor), 0.228 (DCC)
R-Value Work: 0.199 (Depositor), 0.198 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.048	α = 90
b = 134.482	β = 90
c = 137.255	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
MOLREP	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-03-27

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2013-03-27
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description