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Sodium in PDB 6v6z: Crystal Structure of N-(4-((4-Methoxy-N-(2,2,2-Trifluoroethyl)Phenyl) Sulfonamido)Isoquinolin-1-Yl)-N-((4-Methoxyphenyl)Sulfonyl)Glycine Bound to Human KEAP1 Kelch Domain

Protein crystallography data

The structure of Crystal Structure of N-(4-((4-Methoxy-N-(2,2,2-Trifluoroethyl)Phenyl) Sulfonamido)Isoquinolin-1-Yl)-N-((4-Methoxyphenyl)Sulfonyl)Glycine Bound to Human KEAP1 Kelch Domain, PDB code: 6v6z was solved by P.R.Lazzara, B.P.David, A.Ankireddy, B.G.Richardson, K.Dye, K.M.Ratia, S.P.Reddy, T.W.Moore, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.73 / 1.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.360, 75.543, 97.947, 74.55, 77.54, 67.48
R / Rfree (%) 19.2 / 21

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of N-(4-((4-Methoxy-N-(2,2,2-Trifluoroethyl)Phenyl) Sulfonamido)Isoquinolin-1-Yl)-N-((4-Methoxyphenyl)Sulfonyl)Glycine Bound to Human KEAP1 Kelch Domain (pdb code 6v6z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of N-(4-((4-Methoxy-N-(2,2,2-Trifluoroethyl)Phenyl) Sulfonamido)Isoquinolin-1-Yl)-N-((4-Methoxyphenyl)Sulfonyl)Glycine Bound to Human KEAP1 Kelch Domain, PDB code: 6v6z:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 6v6z

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Sodium binding site 1 out of 8 in the Crystal Structure of N-(4-((4-Methoxy-N-(2,2,2-Trifluoroethyl)Phenyl) Sulfonamido)Isoquinolin-1-Yl)-N-((4-Methoxyphenyl)Sulfonyl)Glycine Bound to Human KEAP1 Kelch Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of N-(4-((4-Methoxy-N-(2,2,2-Trifluoroethyl)Phenyl) Sulfonamido)Isoquinolin-1-Yl)-N-((4-Methoxyphenyl)Sulfonyl)Glycine Bound to Human KEAP1 Kelch Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na705

b:25.1
occ:1.00
 O A:HOH968 2.3 23.3 1.0
O A:HOH942 2.3 21.4 1.0
O A:HOH874 2.4 23.4 1.0
O A:HOH945 2.5 19.0 1.0
O A:HOH1041 2.5 32.4 1.0
O A:HOH1005 3.0 24.9 1.0
O A:HOH1000 4.0 21.6 1.0
O A:HOH1079 4.1 35.3 1.0
O A:VAL465 4.2 15.8 1.0
O A:VAL418 4.2 14.9 1.0
O A:HOH832 4.3 23.2 1.0
O A:VAL512 4.3 12.2 1.0
O A:HOH984 4.3 15.7 1.0
O A:VAL606 4.4 15.5 1.0
O A:GLY367 4.5 15.6 1.0
O A:HOH980 4.5 27.3 1.0
O A:ILE559 4.6 15.3 1.0
O A:HOH1010 5.0 20.6 1.0

Sodium binding site 2 out of 8 in 6v6z

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Sodium binding site 2 out of 8 in the Crystal Structure of N-(4-((4-Methoxy-N-(2,2,2-Trifluoroethyl)Phenyl) Sulfonamido)Isoquinolin-1-Yl)-N-((4-Methoxyphenyl)Sulfonyl)Glycine Bound to Human KEAP1 Kelch Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of N-(4-((4-Methoxy-N-(2,2,2-Trifluoroethyl)Phenyl) Sulfonamido)Isoquinolin-1-Yl)-N-((4-Methoxyphenyl)Sulfonyl)Glycine Bound to Human KEAP1 Kelch Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na708

b:32.5
occ:1.00
 O A:HOH1051 2.2 41.6 1.0
O A:TRP450 2.3 16.4 1.0
O A:HOH1028 2.5 32.2 1.0
O A:HOH935 2.5 21.9 1.0
O A:HOH1045 2.7 24.2 1.0
C A:TRP450 3.5 16.3 1.0
N A:TRP450 3.8 15.9 1.0
O A:HOH871 3.8 30.5 1.0
CA A:TRP450 4.1 14.8 1.0
CD2 A:HIS451 4.2 28.3 1.0
NE2 A:HIS451 4.3 30.6 1.0
CB A:TRP450 4.4 14.9 1.0
O A:HOH900 4.5 16.6 1.0
N A:HIS451 4.5 17.0 1.0
CG A:HIS451 4.7 25.9 1.0
CB A:GLU449 4.7 23.5 1.0
CE1 A:HIS451 4.7 30.6 1.0
C A:GLU449 4.7 16.4 1.0
CA A:HIS451 4.8 17.7 1.0
O A:HOH959 4.8 27.0 1.0
CA A:GLU449 4.9 18.9 1.0
ND1 A:HIS451 4.9 29.1 1.0

Sodium binding site 3 out of 8 in 6v6z

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Sodium binding site 3 out of 8 in the Crystal Structure of N-(4-((4-Methoxy-N-(2,2,2-Trifluoroethyl)Phenyl) Sulfonamido)Isoquinolin-1-Yl)-N-((4-Methoxyphenyl)Sulfonyl)Glycine Bound to Human KEAP1 Kelch Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of N-(4-((4-Methoxy-N-(2,2,2-Trifluoroethyl)Phenyl) Sulfonamido)Isoquinolin-1-Yl)-N-((4-Methoxyphenyl)Sulfonyl)Glycine Bound to Human KEAP1 Kelch Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na709

b:23.4
occ:1.00
 O A:HOH834 2.4 22.9 1.0
O A:THR598 2.7 18.1 1.0
O A:HOH908 3.5 26.9 1.0
C A:THR598 3.6 17.3 1.0
O A:HOH1055 3.7 35.2 1.0
CA A:SER599 4.0 16.2 1.0
N A:SER599 4.2 16.1 1.0
OD2 A:ASP579 4.4 21.7 1.0
CB A:SER599 4.5 17.7 1.0
NH2 A:ARG596 4.5 35.2 1.0
O A:HOH911 4.6 23.9 1.0
O A:MET597 4.6 17.5 1.0
CA A:THR598 4.7 16.7 1.0

Sodium binding site 4 out of 8 in 6v6z

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Sodium binding site 4 out of 8 in the Crystal Structure of N-(4-((4-Methoxy-N-(2,2,2-Trifluoroethyl)Phenyl) Sulfonamido)Isoquinolin-1-Yl)-N-((4-Methoxyphenyl)Sulfonyl)Glycine Bound to Human KEAP1 Kelch Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of N-(4-((4-Methoxy-N-(2,2,2-Trifluoroethyl)Phenyl) Sulfonamido)Isoquinolin-1-Yl)-N-((4-Methoxyphenyl)Sulfonyl)Glycine Bound to Human KEAP1 Kelch Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na720

b:36.3
occ:1.00
 O B:VAL465 2.2 17.2 1.0
O B:HOH946 2.2 32.4 1.0
O B:VAL512 2.3 14.4 1.0
O B:HOH962 2.3 28.6 1.0
O B:HOH886 2.5 27.6 1.0
O B:HOH809 2.5 21.1 1.0
C B:VAL512 3.4 13.8 1.0
C B:VAL465 3.4 16.8 1.0
O B:HOH835 4.1 23.1 1.0
O B:HOH885 4.1 20.5 1.0
CB B:ALA466 4.1 20.9 1.0
N B:VAL465 4.2 13.7 1.0
O B:HOH887 4.2 24.2 1.0
CA B:CYS513 4.2 15.0 1.0
N B:CYS513 4.2 15.0 1.0
NA B:NA721 4.2 33.8 1.0
O B:HOH985 4.2 43.2 1.0
N B:ALA466 4.3 16.9 1.0
CA B:ALA466 4.3 17.4 1.0
CA B:VAL512 4.4 13.5 1.0
CA B:VAL465 4.4 14.1 1.0
CB B:VAL512 4.5 14.2 1.0
O B:VAL418 4.6 16.2 1.0
O2 B:FMT718 4.7 37.1 1.0
CG1 B:VAL512 4.7 15.4 1.0
N B:VAL512 4.7 13.3 1.0
CG2 B:ILE559 4.8 15.2 1.0
CB B:CYS513 4.9 16.3 1.0
O1 B:FMT718 4.9 39.9 1.0
O1 B:FMT711 5.0 32.3 1.0
CB B:VAL465 5.0 15.4 1.0

Sodium binding site 5 out of 8 in 6v6z

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Sodium binding site 5 out of 8 in the Crystal Structure of N-(4-((4-Methoxy-N-(2,2,2-Trifluoroethyl)Phenyl) Sulfonamido)Isoquinolin-1-Yl)-N-((4-Methoxyphenyl)Sulfonyl)Glycine Bound to Human KEAP1 Kelch Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of N-(4-((4-Methoxy-N-(2,2,2-Trifluoroethyl)Phenyl) Sulfonamido)Isoquinolin-1-Yl)-N-((4-Methoxyphenyl)Sulfonyl)Glycine Bound to Human KEAP1 Kelch Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na721

b:33.8
occ:1.00
 O1 B:FMT718 2.2 39.9 1.0
O B:HOH809 2.3 21.1 1.0
O1 B:FMT715 2.6 35.5 1.0
O B:ILE559 2.8 17.1 1.0
O B:HOH980 2.9 17.9 1.0
O B:VAL606 3.1 21.5 1.0
C B:FMT715 3.1 35.5 1.0
C B:FMT718 3.2 35.1 1.0
O B:HOH887 3.3 24.2 1.0
O B:HOH962 3.4 28.6 1.0
O2 B:FMT718 3.9 37.1 1.0
C B:ILE559 4.0 16.6 1.0
C B:VAL606 4.0 20.6 1.0
CB B:VAL606 4.2 19.5 1.0
NA B:NA720 4.2 36.3 1.0
CG2 B:ILE559 4.2 15.2 1.0
O2 B:FMT715 4.3 33.8 1.0
O B:HOH822 4.3 31.1 1.0
N B:VAL606 4.4 17.3 1.0
CA B:VAL606 4.4 17.9 1.0
O B:GLY367 4.5 18.2 1.0
N B:ILE559 4.5 15.4 1.0
O B:HOH946 4.5 32.4 1.0
O B:HOH917 4.6 22.7 1.0
O B:HOH886 4.7 27.6 1.0
CA B:ILE559 4.7 15.8 1.0
O B:HOH885 4.8 20.5 1.0
CG1 B:VAL606 4.9 21.6 1.0
O B:HOH835 4.9 23.1 1.0

Sodium binding site 6 out of 8 in 6v6z

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Sodium binding site 6 out of 8 in the Crystal Structure of N-(4-((4-Methoxy-N-(2,2,2-Trifluoroethyl)Phenyl) Sulfonamido)Isoquinolin-1-Yl)-N-((4-Methoxyphenyl)Sulfonyl)Glycine Bound to Human KEAP1 Kelch Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of N-(4-((4-Methoxy-N-(2,2,2-Trifluoroethyl)Phenyl) Sulfonamido)Isoquinolin-1-Yl)-N-((4-Methoxyphenyl)Sulfonyl)Glycine Bound to Human KEAP1 Kelch Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na705

b:21.9
occ:1.00
 O C:VAL465 2.3 19.6 1.0
O C:VAL512 2.3 16.9 1.0
O C:HOH992 2.3 36.4 1.0
O2 C:FMT711 2.5 39.5 1.0
O C:HOH802 2.5 27.5 1.0
O C:HOH954 2.5 18.2 1.0
C C:VAL512 3.5 17.1 1.0
C C:VAL465 3.5 17.2 1.0
C C:FMT711 3.6 37.3 1.0
O1 C:FMT717 3.8 38.7 1.0
O1 C:FMT716 4.0 38.0 1.0
N C:VAL465 4.1 16.9 1.0
CA C:CYS513 4.2 16.8 1.0
N C:CYS513 4.2 16.3 1.0
CA C:VAL465 4.3 16.9 1.0
O C:HOH981 4.3 21.3 1.0
O C:HOH961 4.4 17.9 1.0
CA C:VAL512 4.5 16.7 1.0
N C:ALA466 4.5 18.8 1.0
O C:VAL418 4.6 16.9 1.0
O C:HOH891 4.6 28.8 1.0
CB C:VAL512 4.6 17.7 1.0
O1 C:FMT711 4.7 35.8 1.0
C C:FMT716 4.7 38.1 1.0
O2 C:FMT716 4.7 32.4 1.0
CB C:VAL465 4.7 18.3 1.0
CA C:ALA466 4.8 18.4 1.0
CB C:CYS513 4.8 18.7 1.0
CG1 C:VAL512 4.8 18.6 1.0
N C:VAL512 4.8 15.8 1.0
C C:FMT717 4.9 43.6 1.0
CG2 C:ILE559 4.9 14.6 1.0

Sodium binding site 7 out of 8 in 6v6z

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Sodium binding site 7 out of 8 in the Crystal Structure of N-(4-((4-Methoxy-N-(2,2,2-Trifluoroethyl)Phenyl) Sulfonamido)Isoquinolin-1-Yl)-N-((4-Methoxyphenyl)Sulfonyl)Glycine Bound to Human KEAP1 Kelch Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of N-(4-((4-Methoxy-N-(2,2,2-Trifluoroethyl)Phenyl) Sulfonamido)Isoquinolin-1-Yl)-N-((4-Methoxyphenyl)Sulfonyl)Glycine Bound to Human KEAP1 Kelch Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na708

b:22.3
occ:1.00
 O D:VAL465 2.2 18.3 1.0
O2 D:FMT705 2.4 31.6 1.0
O D:VAL512 2.4 16.4 1.0
O D:HOH942 2.4 28.3 1.0
O D:HOH913 2.5 21.0 1.0
O D:HOH822 2.6 26.3 1.0
C D:FMT705 3.4 33.4 1.0
C D:VAL465 3.4 18.1 1.0
C D:VAL512 3.5 16.1 1.0
O D:HOH816 3.7 31.1 1.0
N D:VAL465 4.0 17.3 1.0
O2 D:FMT719 4.1 38.2 1.0
O D:HOH869 4.1 40.1 1.0
CA D:CYS513 4.1 17.5 1.0
N D:CYS513 4.2 16.3 1.0
CA D:VAL465 4.2 17.8 1.0
O D:HOH943 4.3 23.0 1.0
O D:HOH1006 4.3 35.3 1.0
C D:FMT719 4.4 37.2 1.0
O D:HOH978 4.4 19.1 1.0
N D:ALA466 4.4 18.3 1.0
CA D:VAL512 4.5 16.0 1.0
O1 D:FMT705 4.5 32.9 1.0
CB D:VAL512 4.6 16.9 1.0
CB D:VAL465 4.6 18.6 1.0
O1 D:FMT719 4.6 33.7 1.0
CA D:ALA466 4.7 19.6 1.0
O D:VAL418 4.7 18.2 1.0
O D:HOH915 4.7 25.4 1.0
CG1 D:VAL512 4.7 19.2 1.0
CB D:CYS513 4.7 19.7 1.0
N D:VAL512 4.8 16.1 1.0

Sodium binding site 8 out of 8 in 6v6z

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Sodium binding site 8 out of 8 in the Crystal Structure of N-(4-((4-Methoxy-N-(2,2,2-Trifluoroethyl)Phenyl) Sulfonamido)Isoquinolin-1-Yl)-N-((4-Methoxyphenyl)Sulfonyl)Glycine Bound to Human KEAP1 Kelch Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of N-(4-((4-Methoxy-N-(2,2,2-Trifluoroethyl)Phenyl) Sulfonamido)Isoquinolin-1-Yl)-N-((4-Methoxyphenyl)Sulfonyl)Glycine Bound to Human KEAP1 Kelch Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na710

b:30.6
occ:1.00
 O D:HOH966 2.3 35.9 1.0
O D:HOH973 2.4 40.6 1.0
O D:TRP450 2.4 18.2 1.0
O D:HOH996 2.4 28.1 1.0
O D:HOH951 2.5 24.1 1.0
C D:TRP450 3.6 17.3 1.0
O D:HOH844 3.8 34.4 1.0
N D:TRP450 4.0 17.4 1.0
O D:HOH919 4.2 22.1 1.0
CA D:TRP450 4.2 15.9 1.0
NE2 D:HIS451 4.4 31.7 1.0
CD2 D:HIS451 4.4 30.1 1.0
CB D:TRP450 4.5 16.5 1.0
N D:HIS451 4.6 19.7 1.0
CE1 D:HIS451 4.7 28.9 1.0
O D:HOH1013 4.7 37.2 1.0
CG D:HIS451 4.7 27.2 1.0
CA D:HIS451 4.9 21.1 1.0
ND1 D:HIS451 4.9 27.6 1.0
CB D:GLU449 4.9 22.8 1.0
O D:HOH952 4.9 31.5 1.0
C D:GLU449 4.9 17.8 1.0

Reference:

P.R.Lazzara, A.D.Jain, A.C.Maldonado, B.Richardson, K.J.Skowron, B.P.David, Z.Siddiqui, K.M.Ratia, T.W.Moore. Synthesis and Evaluation of Noncovalent Naphthalene-Based KEAP1-NRF2 Inhibitors. Acs Med.Chem.Lett. V. 11 521 2020.
ISSN: ISSN 1948-5875
PubMed: 32292559
DOI: 10.1021/ACSMEDCHEMLETT.9B00631
Page generated: Tue Oct 8 14:17:10 2024

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