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

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

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

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P51813
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
H88 Query on H88 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	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		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-05-27

Deposition Author(s):

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

Revision History (Full details and data files)

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

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Help and Resources

6I99

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

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)