6V6Z

Crystal structure of N-[(4-methoxyphenyl)sulfonyl]-N-(4-{[(4-methoxyphenyl)sulfonyl]amino}naphthalen-1-yl)glycine bound to human Keap1 Kelch domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

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Literature

Synthesis and Evaluation of Noncovalent Naphthalene-Based KEAP1-NRF2 Inhibitors.

Lazzara, P.R., Jain, A.D., Maldonado, A.C., Richardson, B., Skowron, K.J., David, B.P., Siddiqui, Z., Ratia, K.M., Moore, T.W.

(2020) ACS Med Chem Lett 11: 521-527

  • DOI: 10.1021/acsmedchemlett.9b00631
  • Primary Citation of Related Structures:  
    6V6Z

  • PubMed Abstract: 

    • The oxidative stress response, gated by the protein-protein interaction of KEAP1 and NRF2, has garnered significant interest in the past decade. Misregulation in this pathway has been implicated in disease states such as multiple sclerosis, rheumatoid arthritis, and diabetic chronic wounds ...

    The oxidative stress response, gated by the protein-protein interaction of KEAP1 and NRF2, has garnered significant interest in the past decade. Misregulation in this pathway has been implicated in disease states such as multiple sclerosis, rheumatoid arthritis, and diabetic chronic wounds. Many of the known activators of NRF2 are electrophilic in nature and may operate through several biological pathways rather than solely through the activation of the oxidative stress response. Recently, our lab has reported a nonelectrophilic, monoacidic, naphthalene-based NRF2 activator which exhibited good potency in vitro . Herein, we report a detailed structure-activity relationship of naphthalene-based NRF2 activators, an X-ray crystal structure of our monoacidic KEAP1 inhibitor, and identification of an underexplored area of the NRF2 binding pocket of KEAP1.

    Organizational Affiliation: 

    UICentre for Drug Discovery and University of Illinois Cancer Center, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Kelch-like ECH-associated protein 1A, B, C, D290Homo sapiensMutation(s): 2 
Gene Names: KEAP1, INRF2, KIAA0132, KLHL19
UniProt & NIH Common Fund Data Resources
Find proteins for Q14145 (Homo sapiens)
Explore Q14145 
Go to UniProtKB:  Q14145
PHAROS:  Q14145
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14145
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Q5Y (Subject of Investigation/LOI)
Query on Q5Y
Download Ideal Coordinates CCD File 
G [auth A],
LB [auth D],
TA [auth C],
Z [auth B]		N-[(4-methoxyphenyl)sulfonyl]-N-(4-{[(4-methoxyphenyl)sulfonyl]amino}naphthalen-1-yl)glycine
C26 H24 N2 O8 S2
NVQFDGYHTTZFJR-UHFFFAOYSA-N		 Ligand Interaction
DTT
Query on DTT
Download Ideal Coordinates CCD File 
QB [auth D]2,3-DIHYDROXY-1,4-DITHIOBUTANE
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N		 Ligand Interaction
DTD
Query on DTD
Download Ideal Coordinates CCD File 
UA [auth C]DITHIANE DIOL
C4 H8 O2 S2
YPGMOWHXEQDBBV-IMJSIDKUSA-N		 Ligand Interaction
FMT
Query on FMT
Download Ideal Coordinates CCD File 
AA [auth B],
AB [auth C],
AC [auth D],
BA [auth B],
BB [auth C],
AA [auth B],
AB [auth C],
AC [auth D],
BA [auth B],
BB [auth C],
CA [auth B],
CB [auth C],
DA [auth B],
DB [auth C],
E [auth A],
EA [auth B],
EB [auth C],
F [auth A],
FA [auth B],
FB [auth C],
GA [auth B],
GB [auth C],
H [auth A],
HA [auth B],
HB [auth C],
IA [auth B],
IB [auth D],
J [auth A],
JA [auth B],
JB [auth D],
K [auth A],
KA [auth B],
KB [auth D],
LA [auth B],
MB [auth D],
N [auth A],
NB [auth D],
O [auth A],
OA [auth C],
OB [auth D],
P [auth A],
PA [auth C],
Q [auth A],
QA [auth C],
R [auth A],
RA [auth C],
S [auth A],
SB [auth D],
T [auth B],
TB [auth D],
U [auth B],
UB [auth D],
V [auth B],
VA [auth C],
VB [auth D],
W [auth B],
WA [auth C],
WB [auth D],
X [auth B],
XA [auth C],
XB [auth D],
Y [auth B],
YA [auth C],
YB [auth D],
ZA [auth C],
ZB [auth D]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
I [auth A],
L [auth A],
M [auth A],
MA [auth B],
NA [auth B],
I [auth A],
L [auth A],
M [auth A],
MA [auth B],
NA [auth B],
PB [auth D],
RB [auth D],
SA [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
Q5Y Binding MOAD:  6V6Z IC50: 63 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.36α = 74.55
b = 75.543β = 77.54
c = 97.947γ = 67.48
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United States1R01 AR069541-01A1
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United States1R01 HL136946-01

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2021-04-07
    Changes: Derived calculations, Structure summary