6VQL

CRYSTAL STRUCTURE OF INTERLEUKIN-1 RECEPTOR-ASSOCIATED KINASE 4 (IRAK4-WT) COMPLEX WITH A NICOTINAMIDE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Optimization of Nicotinamides as Potent and Selective IRAK4 Inhibitors with Efficacy in a Murine Model of Psoriasis.

Nair, S.Kumar, S.R.Paidi, V.R.Sistla, R.Kantheti, D.Polimera, S.R.Thangavel, S.Mukherjee, A.J.Das, M.Bhide, R.S.Pitts, W.J.Murugesan, N.Dudhgoankar, S.Nagar, J.Subramani, S.Mazumder, D.Carman, J.A.Holloway, D.A.Li, X.Fereshteh, M.P.Ruepp, S.Palanisamy, K.Mariappan, T.T.Maddi, S.Saxena, A.Elzinga, P.Chimalakonda, A.Ruan, Q.Ghosh, K.Bose, S.Sack, J.Yan, C.Kiefer, S.E.Xie, D.Newitt, J.A.Saravanakumar, S.P.Rampulla, R.A.Barrish, J.C.Carter, P.H.Hynes Jr., J.

(2020) ACS Med Chem Lett 11: 1402-1409

  • DOI: 10.1021/acsmedchemlett.0c00082
  • Primary Citation of Related Structures:  
    6LXY, 6VQL

  • PubMed Abstract: 
  • IRAK4 is an attractive therapeutic target for the treatment of inflammatory conditions. Structure guided optimization of a nicotinamide series of inhibitors has been expanded to explore the IRAK4 front pocket. This has resulted in the identification of compounds such as 12 with improved potency and selectivity ...

    IRAK4 is an attractive therapeutic target for the treatment of inflammatory conditions. Structure guided optimization of a nicotinamide series of inhibitors has been expanded to explore the IRAK4 front pocket. This has resulted in the identification of compounds such as 12 with improved potency and selectivity. Additionally 12 demonstrated activity in a pharmacokinetics/pharmacodynamics (PK/PD) model. Further optimization efforts led to the identification of the highly kinome selective 21 , which demonstrated a robust PD effect and efficacy in a TLR7 driven model of murine psoriasis.


    Organizational Affiliation

    Research & Development, Bristol Myers Squibb, Route 206 & Province Line Road, Princeton, New Jersey 08543, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-1 receptor-associated kinase 4A, B, C, D305Homo sapiensMutation(s): 0 
Gene Names: IRAK4
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWZ3 (Homo sapiens)
Explore Q9NWZ3 
Go to UniProtKB:  Q9NWZ3
PHAROS:  Q9NWZ3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R7S (Subject of Investigation/LOI)
Query on R7S

Download Ideal Coordinates CCD File 
E [auth A], G [auth B], L [auth C], P [auth D]6-[(1,3-benzothiazol-6-yl)amino]-4-(cyclopropylamino)-N-[(2R)-2-fluoro-3-hydroxy-3-methylbutyl]pyridine-3-carboxamide
C21 H24 F N5 O2 S
SHENXRCDBJGWNU-GOSISDBHSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A] , H [auth B] , I [auth B] , J [auth B] , K [auth B] , M [auth C] , N [auth C] , O [auth C] , 
F [auth A], H [auth B], I [auth B], J [auth B], K [auth B], M [auth C], N [auth C], O [auth C], Q [auth D], R [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A, B, C, DL-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A, B, C, DL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.352α = 90
b = 140.827β = 126.2
c = 86.068γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2020-02-05 
  • Released Date: 2020-06-24 
  • Deposition Author(s): Sack, J.S.

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-24
    Type: Initial release
  • Version 1.1: 2020-07-29
    Changes: Database references