4QQE

Crystal structure of WDR5, WD repeat domain 5 in complex with compound SGC-DS-MT-0345

• PDB DOI: https://doi.org/10.2210/pdb4QQE/pdb

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


• Deposited: 2014-06-27 Released: 2014-07-30 
• Deposition Author(s): Dong, A., Dombrovski, L., Wernimont, A., Smil, D., Getlik, M., Senisterra, G., Poda, G., Al-Awar, R., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Brown, P.J., Schapira, M., Vedadi, M., Wu, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.218 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 

Starting Model: experimental

Literature

Crystal structure of WDR5, WD repeat domain 5 in complex with compound SGC-DS-MT-0345

Dombrovski, L., Dong, A., Wernimont, A., Smil, D., Getlik, M., Senisterra, G., Poda, G., Al-Awar, R., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Brown, P.J., Schapira, M., Vedadi, M., Wu, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.02 kDa 
• Atom Count: 2,634 
• Modelled Residue Count: 304 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WD repeat-containing protein 5	A	312	Homo sapiens	Mutation(s): 0  Gene Names: BIG3, WDR5
UniProt & NIH Common Fund Data Resources
Find proteins for P61964 (Homo sapiens) Explore P61964  Go to UniProtKB:  P61964
GTEx:  ENSG00000196363

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
37F	B [auth A]	N-[2-(4-methylpiperazin-1-yl)-5-(quinolin-3-yl)phenyl]-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide C27 H24 F3 N5 O2 BHSUCGLRVZHATB-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNX	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	UNKNOWN ATOM OR ION X

Binding Affinity Annotations
ID	Source	Binding Affinity
37F	BindingDB:  4QQE	Kd: 50 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.218 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.896	α = 90
b = 85.267	β = 90
c = 40.209	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-30 
Deposition Author(s): Dong, A., Dombrovski, L., Wernimont, A., Smil, D., Getlik, M., Senisterra, G., Poda, G., Al-Awar, R., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Brown, P.J., Schapira, M., Vedadi, M., Wu, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2014-07-30
  Type: Initial release
  
• Version 1.1: 2014-10-15
  Changes: Database references, Source and taxonomy
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description