6I99

Bone Marrow Tyrosine Kinase in Chromosome X in complex with a newly designed covalent inhibitor JS24

• PDB DOI: https://doi.org/10.2210/pdb6I99/pdb

• Classification: CYTOSOLIC PROTEIN
• Organism(s): Homo sapiens
• Expression System: Baculovirus expression vector pFastBac1-HM
• Mutation(s): Yes 


• Deposited: 2018-11-22 Released: 2020-05-27 
• Deposition Author(s): Sousa, B.B., Matias, P.M., Marques, M.C., Seixas, J.D., Bernardes, G.J.L.
• Funding Organization(s): European Commission, Royal Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.259 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 

Starting Model: experimental

Literature

Structural and biophysical insights into the mode of covalent binding of rationally designed potent BMX inhibitors

Seixas, J.D., Sousa, B.B., Marques, M.C., Guerreiro, A., Traquete, R., Rodrigues, T., Albuquerque, I.S., Sousa, M.F.Q., Lemos, A.R., Sousa, P.M.F., Bandeiras, T.M., Wu, D., Doyle, S.K., Robinson, C.V., Koehler, A.N., Corzana, F., Matias, P.M., Bernardes, G.J.L.

(2020) Chem Biol 

• DOI: https://doi.org/10.1039/D0CB00033G

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 66.21 kDa 
• Atom Count: 4,510 
• Modelled Residue Count: 527 
• Deposited Residue Count: 556 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytoplasmic tyrosine-protein kinase BMX	A, B	278	Homo sapiens	Mutation(s): 4  Gene Names: BMX EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P51813 (Homo sapiens) Explore P51813  Go to UniProtKB:  P51813
PHAROS:  P51813 GTEx:  ENSG00000102010

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H88	C [auth A], D [auth B]	~{N}-[2-methyl-5-[8-[4-(methylsulfonylamino)phenyl]-2-oxidanylidene-benzo[h][1,6]naphthyridin-1-yl]phenyl]-3-oxidanyl-propanamide C29 H26 N4 O5 S PBOKXQRUWSFTHG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.259 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.714	α = 90
b = 63.29	β = 104.55
c = 74.962	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-05-27 
Deposition Author(s): Sousa, B.B., Matias, P.M., Marques, M.C., Seixas, J.D., Bernardes, G.J.L.

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Funding Organization	Location	Grant Number
European Commission		702428
Royal Society	United Kingdom	676832
European Commission		675007

Revision History  

• Version 1.0: 2020-05-27
  Type: Initial release
  
• Version 1.1: 2020-11-04
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary