5EAL

Crystal structure of human WDR5 in complex with compound 9h

• PDB DOI: https://doi.org/10.2210/pdb5EAL/pdb

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


• Deposited: 2015-10-16 Released: 2015-11-04 
• Deposition Author(s): DONG, A., DOMBROVSKI, L., SMIL, D., GETLIK, M., BOLSHAN, Y., WALKER, J.R., SENISTERRA, G., PODA, G., AL-AWAR, R., SCHAPIRA, M., VEDADI, M., Bountra, C., Edwards, A.M., Arrowsmith, C.H., BROWN, P.J., WU, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.211 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 

Literature

Crystal structure of human WDR5 in complex with compound 9h

DOMBROVSKI, L., DONG, A., SMIL, D., GETLIK, M., BOLSHAN, Y., WALKER, J.R., SENISTERRA, G., PODA, G., AL-AWAR, R., SCHAPIRA, M., VEDADI, M., Bountra, C., Edwards, A.M., Arrowsmith, C.H., BROWN, P.J., WU, H., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 70.64 kDa 
• Atom Count: 5,390 
• Modelled Residue Count: 608 
• Deposited Residue Count: 624 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5ML	AA [auth B], C [auth A]	3-methyl-~{N}-[2-(4-methylpiperazin-1-yl)-5-quinolin-3-yl-phenyl]benzamide C28 H28 N4 O SGTMEYAZQRHDJV-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	BA [auth B], CA [auth B], DA [auth B], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], L [auth A], M [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNX	KA [auth B], LA [auth B], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	UNKNOWN ATOM OR ION X

Binding Affinity Annotations
ID	Source	Binding Affinity
5ML	BindingDB:  5EAL	Kd: 720 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.211 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.191	α = 110.67
b = 60.962	β = 90.43
c = 64.126	γ = 109.47

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-04 
Deposition Author(s): DONG, A., DOMBROVSKI, L., SMIL, D., GETLIK, M., BOLSHAN, Y., WALKER, J.R., SENISTERRA, G., PODA, G., AL-AWAR, R., SCHAPIRA, M., VEDADI, M., Bountra, C., Edwards, A.M., Arrowsmith, C.H., BROWN, P.J., WU, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2015-11-04
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description