5W5O | pdb_00005w5o

Identification of potent and selective RIPK2 inhibitors for the treatment of inflammatory diseases.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 
    0.252 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: other
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wwPDB Validation 3D Report Full Report

Validation slider image for 5W5O

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Identification of Potent and Selective RIPK2 Inhibitors for the Treatment of Inflammatory Diseases.

He, X.Da Ros, S.Nelson, J.Zhu, X.Jiang, T.Okram, B.Jiang, S.Michellys, P.Y.Iskandar, M.Espinola, S.Jia, Y.Bursulaya, B.Kreusch, A.Gao, M.Y.Spraggon, G.Baaten, J.Clemmer, L.Meeusen, S.Huang, D.Hill, R.Nguyen-Tran, V.Fathman, J.Liu, B.Tuntland, T.Gordon, P.Hollenbeck, T.Ng, K.Shi, J.Bordone, L.Liu, H.

(2017) ACS Med Chem Lett 8: 1048-1053

  • DOI: https://doi.org/10.1021/acsmedchemlett.7b00258
  • Primary Citation Related Structures: 
    5W5J, 5W5O

  • PubMed Abstract: 

    NOD2 (nucleotide-binding oligomerization domain-containing protein 2) is an internal pattern recognition receptor that recognizes bacterial peptidoglycan and stimulates host immune responses. Dysfunction of NOD2 pathway has been associated with a number of autoinflammatory disorders. To date, direct inhibitors of NOD2 have not been described due to technical challenges of targeting the oligomeric protein complex. Receptor interacting protein kinase 2 (RIPK2) is an intracellular serine/threonine/tyrosine kinase, a key signaling partner, and an obligate kinase for NOD2. As such, RIPK2 represents an attractive target to probe the pathological roles of NOD2 pathway. To search for selective RIPK2 inhibitors, we employed virtual library screening (VLS) and structure based design that eventually led to a potent and selective RIPK2 inhibitor 8 with excellent oral bioavailability, which was used to evaluate the effects of inhibition of RIPK2 in various in vitro assays and ex vivo and in vivo pharmacodynamic models.


  • Organizational Affiliation
    • Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States.

Macromolecule Content 

  • Total Structure Weight: 578.1 kDa 
  • Atom Count: 35,681 
  • Modeled Residue Count: 4,399 
  • Deposited Residue Count: 4,960 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Receptor-interacting serine/threonine-protein kinase 2
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
310Homo sapiensMutation(s): 0 
Gene Names: RIPK2CARDIAKRICKRIP2UNQ277/PRO314/PRO34092
EC: 2.7.11.1 (PDB Primary Data), 2.7.10.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O43353 (Homo sapiens)
Explore O43353 
Go to UniProtKB:  O43353
PHAROS:  O43353
GTEx:  ENSG00000104312 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43353
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9XA

Query on 9XA



Download:Ideal Coordinates CCD File
AA [auth K]
BA [auth L]
CA [auth M]
DA [auth N]
EA [auth O]
AA [auth K],
BA [auth L],
CA [auth M],
DA [auth N],
EA [auth O],
FA [auth P],
Q [auth A],
R [auth B],
S [auth C],
T [auth D],
U [auth E],
V [auth F],
W [auth G],
X [auth H],
Y [auth I],
Z [auth J]
4-{6-(tert-butylsulfonyl)-7-[2-(4-methylpiperazin-1-yl)ethoxy]imidazo[1,2-a]pyridin-3-yl}-6-chloropyridin-2-amine
C23 H31 Cl N6 O3 S
PIIVPMZRLRQOTG-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
9XA BindingDB:  5W5O IC50: 8 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free:  0.252 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.308α = 90.15
b = 107.475β = 89.77
c = 210.193γ = 89.96
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-25
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references
  • Version 1.3: 2024-04-03
    Changes: Refinement description