3SMR

Crystal structure of human WD repeat domain 5 with compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
WD repeat-containing protein 5
A, B, C, D
312Homo sapiensMutation(s): 0 
Gene Names: WDR5 (BIG3)
Find proteins for P61964 (Homo sapiens)
Go to Gene View: WDR5
Go to UniProtKB:  P61964
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NP7
Query on NP7

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Download CCD File 
A, B, C, D
2-chloro-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide
C18 H19 Cl N4 O3
WOGZFCMBPXJNFI-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

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Download CCD File 
A, B, C, D
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NP7Kd: 6900 - 7000 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 204.171α = 90.00
b = 93.467β = 107.24
c = 64.786γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MOLREPphasing
StructureStudiodata collection
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2011-08-31
    Type: Initial release
  • Version 1.1: 2018-05-16
    Type: Data collection, Database references