6VXR | pdb_00006vxr

Structure of Maternal embryonic leucine zipper kinase bound to LDSM276

• PDB DOI: https://doi.org/10.2210/pdb6VXR/pdb

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


• Deposited: 2020-02-24 Released: 2020-07-29 
• Deposition Author(s): Counago, R.M., Takarada, J.E., dos Reis, C.V., Gama, F.H., Azevedo, H., Mascarello, A., Guimaraes, C.R., Structural Genomics Consortium (SGC)
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP), Brazilian National Council for Scientific and Technological Development (CNPq)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.248 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Structure of Maternal embryonic leucine zipper kinase bound to LDSM276

Counago, R.M., Takarada, J.E., dos Reis, C.V., Guimaraes, C.R., Azevedo, H., Mascarello, A., Gama, F.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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 39.74 kDa 
• Atom Count: 2,512 
• Modeled Residue Count: 309 
• Deposited Residue Count: 339 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maternal embryonic leucine zipper kinase	A	339	Homo sapiens	Mutation(s): 0  Gene Names: MELK, KIAA0175 EC: 2.7.11.1 (PDB Primary Data), 2.7.10.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q14680 (Homo sapiens) Explore Q14680  Go to UniProtKB:  Q14680
PHAROS:  Q14680 GTEx:  ENSG00000165304

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F7D (Subject of Investigation/LOI)	B [auth A]	(7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5,8-di(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one C19 H15 F2 N5 O2 KDZIESJUFYBJGD-LLVKDONJSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.248 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.124	α = 90
b = 70.159	β = 90
c = 102.067	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-07-29 
Deposition Author(s): Counago, R.M., Takarada, J.E., dos Reis, C.V., Gama, F.H., Azevedo, H., Mascarello, A., Guimaraes, C.R., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2013/50724-5
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	465651/2014-3
Sao Paulo Research Foundation (FAPESP)	Brazil	2014/50897-0

Revision History  

• Version 1.0: 2020-07-29
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description