Sodium in PDB 8pkv: Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (Ortho-Wrcdeetgec)

The structure of Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (Ortho-Wrcdeetgec), PDB code: 8pkv was solved by M.B.Braun, L.Bischof, M.D.Hartmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.19 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	162.957, 68.861, 77.95, 90, 117.66, 90
R / Rfree (%)	15.7 / 19.2

The structure of Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (Ortho-Wrcdeetgec) also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (Ortho-Wrcdeetgec) (pdb code 8pkv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (Ortho-Wrcdeetgec), PDB code: 8pkv:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (Ortho-Wrcdeetgec)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (Ortho-Wrcdeetgec) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na712 b:44.2 occ:1.00 OE1 A:GLU449 2.3 48.7 1.0 NE2 A:HIS451 2.3 55.4 1.0 NH1 A:ARG447 2.6 60.5 0.5 OE2 A:GLU444 2.7 63.1 1.0 CD2 A:HIS451 3.0 52.0 1.0 CD A:GLU444 3.3 60.7 1.0 NE A:ARG447 3.4 53.2 0.5 CD A:GLU449 3.4 51.8 1.0 CD A:ARG447 3.5 48.6 0.5 CE1 A:HIS451 3.5 56.8 1.0 OE1 A:GLU444 3.6 69.6 1.0 CB A:GLU449 3.8 36.1 1.0 CZ A:ARG447 3.8 57.5 0.5 CD A:ARG447 4.0 49.3 0.5 CG A:GLU449 4.2 46.5 1.0 CG A:HIS451 4.3 48.2 1.0 CG A:GLU444 4.3 46.2 1.0 NE A:ARG447 4.3 54.4 0.5 OE2 A:GLU449 4.4 56.5 1.0 CB A:ARG447 4.4 39.8 0.5 ND1 A:HIS451 4.5 54.4 1.0 CB A:ARG447 4.5 40.5 0.5 CG A:ARG447 4.5 45.8 0.5 CZ A:ARG447 4.5 56.6 0.5 CG A:ARG447 4.5 45.1 0.5 CB A:GLU444 4.8 37.5 1.0 NH2 A:ARG447 4.8 57.3 0.5

Sodium binding site 2 out of 8 in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (Ortho-Wrcdeetgec)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (Ortho-Wrcdeetgec) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na713 b:33.7 occ:1.00 O A:CYS406 2.6 27.7 1.0 O A:HOH879 2.7 30.0 1.0 N A:LEU393 3.1 23.1 1.0 O A:LEU393 3.2 25.7 1.0 CA A:ALA392 3.4 23.5 1.0 N A:PRO408 3.6 24.8 1.0 CA A:PRO408 3.6 23.6 1.0 CB A:PRO408 3.7 26.5 1.0 C A:CYS406 3.7 24.6 1.0 CB A:ALA392 3.7 26.0 1.0 C A:ALA392 3.8 24.8 1.0 C A:ALA407 3.8 26.1 1.0 C A:LEU393 3.9 25.7 1.0 CD A:PRO408 3.9 26.9 1.0 CA A:LEU393 4.0 25.2 1.0 O A:ALA407 4.1 26.9 1.0 N A:CYS406 4.2 26.2 1.0 CG A:PRO408 4.4 27.4 1.0 CB A:LEU393 4.5 22.8 1.0 CA A:ALA407 4.6 26.7 1.0 CA A:CYS406 4.6 25.2 1.0 N A:ALA407 4.6 26.4 1.0 N A:ALA392 4.7 26.9 1.0 O A:SER391 4.7 25.4 1.0 OD2 A:ASP394 4.9 30.4 1.0 OD1 A:ASP394 4.9 29.2 1.0 CB A:PRO405 5.0 31.5 1.0

Sodium binding site 3 out of 8 in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (Ortho-Wrcdeetgec)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (Ortho-Wrcdeetgec) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na714 b:47.0 occ:1.00 OG A:SER508 2.7 29.9 0.7 O A:HOH809 3.1 56.9 1.0 OG A:SER555 3.2 37.7 1.0 O A:SER508 3.2 28.2 1.0 C A:SER508 3.4 26.4 1.0 O A:HOH818 3.5 50.1 1.0 CB A:TYR525 3.5 30.5 1.0 CB A:SER508 3.6 28.8 0.3 CB A:SER508 3.7 26.6 0.7 N A:GLY509 3.8 26.6 1.0 OG A:SER508 3.8 29.5 0.3 CA A:GLY509 3.9 24.8 1.0 CD2 A:TYR525 4.1 31.1 1.0 CA A:SER508 4.1 27.3 0.3 CA A:SER508 4.1 26.9 0.7 CG A:TYR525 4.3 30.6 1.0 CB A:SER555 4.5 31.7 1.0 N A:TYR525 4.6 28.2 1.0 NE A:ARG483 4.6 41.2 1.0 CA A:TYR525 4.6 28.5 1.0 NH1 A:ARG415 4.7 29.2 1.0 O A:TYR525 4.9 30.6 1.0 N A:SER508 4.9 26.7 1.0 C A:GLY509 5.0 27.2 1.0

Sodium binding site 4 out of 8 in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (Ortho-Wrcdeetgec)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (Ortho-Wrcdeetgec) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na715 b:68.1 occ:1.00 O A:HOH919 2.6 51.7 1.0 OG1 A:THR545 2.8 42.5 1.0 O A:HOH955 2.8 60.4 1.0 O A:THR543 2.9 40.0 1.0 O A:ARG536 3.2 34.3 1.0 CB A:THR545 3.3 37.3 1.0 N A:THR545 3.6 34.8 1.0 C A:THR543 3.7 40.7 1.0 N A:ASP538 3.9 40.5 1.0 CB A:ASP538 3.9 55.2 1.0 C A:TRP544 4.0 36.9 1.0 CA A:THR545 4.1 33.3 1.0 CA A:TRP544 4.2 35.3 1.0 C A:ARG536 4.2 31.1 1.0 N A:TRP544 4.3 38.0 1.0 CG2 A:THR543 4.4 52.2 1.0 CB A:THR543 4.4 50.3 1.0 C A:TYR537 4.5 36.2 1.0 CA A:ASP538 4.5 45.3 1.0 CA A:TYR537 4.5 32.4 1.0 CA A:THR543 4.6 47.5 1.0 CG2 A:THR545 4.6 44.1 1.0 OG1 A:THR541 4.6 50.3 1.0 O A:TRP544 4.7 42.8 1.0 N A:TYR537 4.8 30.2 1.0 CG A:ARG536 4.9 41.1 1.0 NE A:ARG536 5.0 48.8 1.0

Sodium binding site 5 out of 8 in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (Ortho-Wrcdeetgec)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (Ortho-Wrcdeetgec) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na716 b:56.6 occ:1.00 OG A:SER340 2.6 25.7 0.5 O A:LEU358 2.8 29.2 1.0 O A:HOH1029 3.0 59.3 1.0 O A:HOH912 3.0 46.2 1.0 CB A:SER340 3.2 33.0 0.5 CB A:SER340 3.2 24.4 0.5 O A:GLN359 3.3 27.2 0.5 OG A:SER340 3.5 35.3 0.5 C A:GLN359 3.7 25.3 0.5 O A:GLN359 3.7 33.0 0.5 C A:GLN359 3.8 28.1 0.5 CD A:PRO361 3.8 27.0 1.0 C A:LEU358 3.9 27.1 1.0 O A:HOH918 3.9 51.9 1.0 N A:PRO361 4.0 25.3 1.0 N A:VAL360 4.0 27.3 1.0 C A:VAL360 4.1 24.4 1.0 CA A:VAL360 4.1 26.8 1.0 CG A:PRO361 4.2 30.0 1.0 O A:HOH834 4.2 52.0 1.0 CA A:GLN359 4.4 29.3 0.5 CA A:GLN359 4.4 27.0 0.5 CA A:SER340 4.6 26.4 0.5 CA A:SER340 4.6 30.0 0.5 CB A:ASP357 4.6 30.2 1.0 N A:GLN359 4.6 28.6 0.5 N A:GLN359 4.6 27.6 0.5 O A:HOH1058 4.7 61.2 1.0 CA A:PRO361 4.7 26.0 1.0 OD2 A:ASP357 4.8 39.3 1.0 O A:VAL360 4.8 27.5 1.0 CA A:LEU358 5.0 27.2 1.0 CB A:PRO361 5.0 28.0 1.0

Sodium binding site 6 out of 8 in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (Ortho-Wrcdeetgec)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (Ortho-Wrcdeetgec) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na717 b:47.9 occ:1.00 O A:GLY367 2.7 28.2 1.0 O A:HOH934 2.7 38.9 1.0 O A:HOH984 2.8 30.0 1.0 O A:HOH852 3.1 40.9 1.0 CL A:CL705 3.1 57.8 1.0 O A:HOH1011 3.2 58.5 1.0 CG2 A:VAL418 3.7 32.8 1.0 C A:GLY367 3.9 25.4 1.0 N A:GLY367 4.0 25.6 1.0 O A:VAL418 4.1 25.6 1.0 O A:HOH832 4.1 44.4 1.0 CB A:ALA366 4.1 25.0 1.0 O A:HOH917 4.3 33.9 1.0 O A:VAL606 4.4 24.5 0.5 O A:HOH904 4.5 36.1 1.0 O A:VAL606 4.5 24.6 0.5 CA A:GLY367 4.5 23.9 1.0 O A:HOH931 4.6 34.9 1.0 CA A:ALA366 4.8 24.0 1.0 C A:ALA366 4.8 23.0 1.0 O A:HOH998 4.8 33.9 1.0 N A:VAL418 4.8 23.2 1.0 C A:VAL418 4.9 24.1 1.0 N A:CYS368 4.9 23.5 1.0 CB A:VAL418 5.0 26.7 1.0 O A:HOH1024 5.0 44.4 1.0

Sodium binding site 7 out of 8 in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (Ortho-Wrcdeetgec)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (Ortho-Wrcdeetgec) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na703 b:75.5 occ:0.50 SG B:CYS434 2.6 52.7 0.5 SG B:CYS434 2.7 42.3 0.5 CB B:CYS434 3.1 37.8 0.5 CB B:CYS434 3.2 47.6 0.5 CA B:CYS434 4.7 35.2 0.5 CA B:CYS434 4.7 40.8 0.5

Sodium binding site 8 out of 8 in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (Ortho-Wrcdeetgec)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (Ortho-Wrcdeetgec) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na704 b:54.4 occ:1.00 O2 B:GOL707 2.7 46.5 1.0 O B:VAL604 2.9 42.1 1.0 O B:HOH865 2.9 42.9 1.0 O B:HOH812 3.0 50.5 1.0 C2 B:GOL707 3.1 55.0 1.0 O B:LEU365 3.1 39.5 1.0 O3 B:GOL707 3.2 57.5 1.0 O B:HOH850 3.5 41.3 1.0 O B:HOH855 3.6 38.2 1.0 C3 B:GOL707 3.8 57.2 1.0 CA B:ALA366 3.8 37.8 1.0 CA B:GLY605 3.9 40.3 1.0 C B:VAL604 4.0 41.0 1.0 C B:LEU365 4.1 34.8 1.0 CB B:ALA366 4.3 38.8 1.0 N B:GLY605 4.4 41.0 1.0 N B:ALA366 4.5 36.4 1.0 C1 B:GOL707 4.5 54.0 1.0 O B:HOH837 4.6 40.7 1.0 O1 B:GOL707 4.7 53.9 1.0 N B:GLY367 4.7 44.4 1.0 N B:VAL606 4.8 43.6 1.0 O B:LEU557 4.8 46.7 1.0 C B:ALA366 4.8 41.8 1.0 O B:HOH861 4.8 56.8 1.0 C B:GLY605 4.9 42.5 1.0

F.Fonseca Lopez, J.Miao, J.Damjanovic, L.Bischof, M.B.Braun, Y.Ling, M.D.Hartmann, Y.S.Lin, J.A.Kritzer. Computational Prediction of Cyclic Peptide Structural Ensembles and Application to the Design of KEAP1 Binders. J.Chem.Inf.Model. 2023.
ISSN: ESSN 1549-960X
PubMed: 37917529
DOI: 10.1021/ACS.JCIM.3C01337