5J5S | pdb_00005j5s

Src kinase in complex with a sulfonamide inhibitor

PDB DOI: https://doi.org/10.2210/pdb5J5S/pdb

Classification: Transferase/Transferase Inhibitor
Organism(s): Gallus gallus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-04-03 Released: 2016-06-01
Deposition Author(s): Lebedev, I., Feldman, H.C., Georghiou, G., Maly, D.J., Seeliger, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.216 (Depositor), 0.216 (DCC)
R-Value Work:
0.167 (Depositor), 0.171 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Structural and Functional Analysis of the Allosteric Modulation of IRE1a with ATP-Competitive Kinase Inhibitors

Feldman, H.C., Tong, M., Wang, L., Meza-Acevedo, R., Gobillot, T.A., Gliedt, M.J., Hari, S.B., Mitra, A.K., Backes, B.J., Papa, F.R., Seeliger, M.A., Maly, D.J.

To be published.

Macromolecule Content

Total Structure Weight: 66.46 kDa
Atom Count: 4,499
Modeled Residue Count: 516
Deposited Residue Count: 572
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase Src	A, B	286	Gallus gallus	Mutation(s): 0 Gene Names: SRC EC: 2.7.10.2
UniProt
Find proteins for P00523 (Gallus gallus) Explore P00523 Go to UniProtKB: P00523
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00523
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6G3 Query on 6G3 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	N-{4-[8-amino-3-(propan-2-yl)imidazo[1,5-a]pyrazin-1-yl]naphthalen-1-yl}-N'-[3-(trifluoromethyl)phenyl]urea C₂₇ H₂₃ F₃ N₆ O MEJKZYOOTMLMBA-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: 2.15 Å
R-Value Free: 0.216 (Depositor), 0.216 (DCC)
R-Value Work: 0.167 (Depositor), 0.171 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.21	α = 100.6
b = 63.551	β = 90.61
c = 73.664	γ = 90.96

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-06-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-06-01
Type: Initial release
Version 1.1: 2017-11-22
Changes: Derived calculations, Refinement description
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.