Macromolecule Content

Total Structure Weight: 139.90 kDa
Atom Count: 8230
Residue Count: 1011
Unique protein chains: 1

6R5F

Crystal structure of RIP1 kinase in complex with DHP77

DOI: 10.2210/pdb6R5F/pdb

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

Deposited: 2019-03-25 Released: 2019-05-01
Deposition Author(s): Thorpe, J.H., Campobasso, N., Harris, P.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.25 Å
R-Value Free: 0.289
R-Value Work: 0.243
R-Value Observed: 0.245

wwPDB Validation 3D Report Full Report

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

Literature

Discovery and Lead-Optimization of 4,5-Dihydropyrazoles as Mono-Kinase Selective, Orally Bioavailable and Efficacious Inhibitors of Receptor Interacting Protein 1 (RIP1) Kinase.

Harris, P.A., Faucher, N., George, N., Eidam, P.M., King, B.W., White, G.V., Anderson, N.A., Bandyopadhyay, D., Beal, A.M., Beneton, V., Berger, S.B., Campobasso, N., Campos, S., Capriotti, C.A., Cox, J.A., Daugan, A., Donche, F., Fouchet, M.H., Finger, J.N., Geddes, B., Gough, P.J., Grondin, P., Hoffman, B.L., Hoffman, S.J., Hutchinson, S.E., Jeong, J.U., Jigorel, E., Lamoureux, P., Leister, L.K., Lich, J.D., Mahajan, M.K., Meslamani, J., Mosley, J.E., Nagilla, R., Nassau, P.M., Ng, S.L., Ouellette, M.T., Pasikanti, K.K., Potvain, F., Reilly, M.A., Rivera, E.J., Sautet, S., Schaeffer, M.C., Sehon, C.A., Sun, H., Thorpe, J.H., Totoritis, R.D., Ward, P., Wellaway, N., Wisnoski, D.D., Woolven, J.M., Bertin, J., Marquis, R.W.

(2019) J Med Chem 62: 5096-5110

PubMed: 31013427 Search on PubMed
DOI: 10.1021/acs.jmedchem.9b00318
Primary Citation of Related Structures:
6OCQ, 6R5F

PubMed Abstract:

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-interacting serine/threonine-protein kinase 1	A, B, C, D	303	Homo sapiens	Mutation(s): 4 Gene Names: RIPK1, RIP, RIP1 EC: 2.7.11.1
Find proteins for Q13546 (Homo sapiens) Explore Q13546 Go to UniProtKB: Q13546
NIH Common Fund Data Resources
PHAROS Q13546 GTEx ENSG00000137275
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JSW Query on JSW Download CCD File	A, B, C, D	[(5~{S})-5-[3,5-bis(fluoranyl)phenyl]pyrazolidin-1-yl]-[1-(5-methyl-1,3,4-oxadiazol-2-yl)piperidin-4-yl]methanone C₁₈ H₂₁ F₂ N₅ O₂ KYFXWICBRBBWQQ-INIZCTEOSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.25 Å
R-Value Free: 0.289
R-Value Work: 0.243
R-Value Observed: 0.245
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.858	α = 90
b = 138.919	β = 96.5
c = 96.534	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
AutoPROC	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2019-03-25
Released Date: 2019-05-01

Deposition Author(s):

Revision History

Version 1.0: 2019-05-01
Type: Initial release
Version 1.1: 2019-06-05
Changes: Data collection, Database references
Version 1.2: 2019-08-21
Changes: Data collection

RCSB PDB is 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.