5TX5

Rip1 Kinase ( flag 1-294, C34A, C127A, C233A, C240A) with GSK772

PDB DOI: https://doi.org/10.2210/pdb5TX5/pdb

Classification: transferase/transferase inhibitor
Organism(s): Homo sapiens
Expression System: unidentified baculovirus
Mutation(s): Yes

Deposited: 2016-11-15 Released: 2017-07-05
Deposition Author(s): Campobasso, N., Ward, P., Thrope, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free: 0.240
R-Value Work: 0.197
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Discovery of a First-in-Class Receptor Interacting Protein 1 (RIP1) Kinase Specific Clinical Candidate (GSK2982772) for the Treatment of Inflammatory Diseases.

Harris, P.A., Berger, S.B., Jeong, J.U., Nagilla, R., Bandyopadhyay, D., Campobasso, N., Capriotti, C.A., Cox, J.A., Dare, L., Dong, X., Eidam, P.M., Finger, J.N., Hoffman, S.J., Kang, J., Kasparcova, V., King, B.W., Lehr, R., Lan, Y., Leister, L.K., Lich, J.D., MacDonald, T.T., Miller, N.A., Ouellette, M.T., Pao, C.S., Rahman, A., Reilly, M.A., Rendina, A.R., Rivera, E.J., Schaeffer, M.C., Sehon, C.A., Singhaus, R.R., Sun, H.H., Swift, B.A., Totoritis, R.D., Vossenkamper, A., Ward, P., Wisnoski, D.D., Zhang, D., Marquis, R.W., Gough, P.J., Bertin, J.

(2017) J Med Chem 60: 1247-1261

PubMed: 28151659 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.6b01751
Primary Citation of Related Structures:
5TX5

PubMed Abstract:

Macromolecule Content

Total Structure Weight: 69.95 kDa
Atom Count: 4,220
Modelled Residue Count: 522
Deposited Residue Count: 606
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-interacting serine/threonine-protein kinase 1	A, B	303	Homo sapiens	Mutation(s): 4 Gene Names: RIPK1, RIP, RIP1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13546 (Homo sapiens) Explore Q13546 Go to UniProtKB: Q13546
PHAROS: Q13546
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13546
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7MJ Query on 7MJ 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]	3-benzyl-N-[(3S)-5-methyl-4-oxo-2,3,4,5-tetrahydro-1,5-benzoxazepin-3-yl]-1H-1,2,4-triazole-5-carboxamide C₂₀ H₁₉ N₅ O₃ LYPAFUINURXJSG-AWEZNQCLSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free: 0.240
R-Value Work: 0.197
R-Value Observed: 0.200
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.774	α = 90
b = 101.246	β = 90
c = 129.753	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-07-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-07-05
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.