3SMR | pdb_00003smr

Crystal structure of human WD repeat domain 5 with compound

• PDB DOI: https://doi.org/10.2210/pdb3SMR/pdb

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


• Deposited: 2011-06-28 Released: 2011-08-31 
• Deposition Author(s): Dong, A., Dombrovski, L., Wasney, G.A., Tempel, W., Senisterra, G., Bolshan, Y., Smil, D., Nguyen, K.T., Hajian, T., Poda, G., Al-Awar, R., Bountra, C., Weigelt, J., Edwards, A.M., Brown, P.J., Schapira, M., Arrowsmith, C.H., Vedadi, M., Wu, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.206 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Small-molecule inhibition of MLL activity by disruption of its interaction with WDR5.

Senisterra, G., Wu, H., Allali-Hassani, A., Wasney, G.A., Barsyte-Lovejoy, D., Dombrovski, L., Dong, A., Nguyen, K.T., Smil, D., Bolshan, Y., Hajian, T., He, H., Seitova, A., Chau, I., Li, F., Poda, G., Couture, J.F., Brown, P.J., Al-Awar, R., Schapira, M., Arrowsmith, C.H., Vedadi, M.

(2013) Biochem J 449: 151-159

• PubMed: 22989411 
• DOI: https://doi.org/10.1042/BJ20121280
• Primary Citation Related Structures: 
  3SMR, 3UR4


• PubMed Abstract: 
  

  WDR5 (WD40 repeat protein 5) is an essential component of the human trithorax-like family of SET1 [Su(var)3-9 enhancer-of-zeste trithorax 1] methyltransferase complexes that carry out trimethylation of histone 3 Lys4 (H3K4me3), play key roles in development and are abnormally expressed in many cancers. In the present study, we show that the interaction between WDR5 and peptides from the catalytic domain of MLL (mixed-lineage leukaemia protein) (KMT2) can be antagonized with a small molecule. Structural and biophysical analysis show that this antagonist binds in the WDR5 peptide-binding pocket with a Kd of 450 nM and inhibits the catalytic activity of the MLL core complex in vitro. The degree of inhibition was enhanced at lower protein concentrations consistent with a role for WDR5 in directly stabilizing the MLL multiprotein complex. Our data demonstrate inhibition of an important protein-protein interaction and form the basis for further development of inhibitors of WDR5-dependent enzymes implicated in MLL-rearranged leukaemias or other cancers.

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Organizational Affiliation: 
• Structural Genomics Consortium, 101 College Street, Toronto, Ontario, Canada.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 140.09 kDa 
• Atom Count: 10,411 
• Modeled Residue Count: 1,211 
• Deposited Residue Count: 1,248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WD repeat-containing protein 5	A, B, C, D	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NP7	E [auth A], LA [auth C], U [auth B], XA [auth D]	2-chloro-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide C18 H19 Cl N4 O3 WOGZFCMBPXJNFI-UHFFFAOYSA-N
EDO	AA [auth B], AB [auth D], BB [auth D], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], MA [auth C], NA [auth C], OA [auth C], PA [auth C], QA [auth C], V [auth B], W [auth B], X [auth B], Y [auth B], YA [auth D], Z [auth B], ZA [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
UNX	BA [auth B], CA [auth B], CB [auth D], DA [auth B], DB [auth D], EA [auth B], EB [auth D], FA [auth B], FB [auth D], GA [auth B], GB [auth D], HA [auth B], HB [auth D], IA [auth B], IB [auth D], JA [auth B], JB [auth D], KA [auth B], KB [auth D], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], RA [auth C], S [auth A], SA [auth C], T [auth A], TA [auth C], UA [auth C], VA [auth C], WA [auth C]	UNKNOWN ATOM OR ION X

Binding Affinity Annotations
ID	Source	Binding Affinity
NP7	BindingDB:  3SMR	Kd: min: 4000, max: 1.20e+4 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.206 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 204.171	α = 90
b = 93.467	β = 107.24
c = 64.786	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-31 
Deposition Author(s): Dong, A., Dombrovski, L., Wasney, G.A., Tempel, W., Senisterra, G., Bolshan, Y., Smil, D., Nguyen, K.T., Hajian, T., Poda, G., Al-Awar, R., Bountra, C., Weigelt, J., Edwards, A.M., Brown, P.J., Schapira, M., Arrowsmith, C.H., Vedadi, M., Wu, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2011-08-31
  Type: Initial release
  
• Version 1.1: 2018-05-16
  Changes: Data collection, Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description