Chlorine in PDB 7ofa: KEAP1 Kelch Domain Bound to A Small Molecule Fragment

The structure of KEAP1 Kelch Domain Bound to A Small Molecule Fragment, PDB code: 7ofa was solved by D.Narayanan, A.Bach, M.Gajhede, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.75 / 2.22
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	103.505, 103.505, 55.746, 90, 90, 120
R / Rfree (%)	20.9 / 24.2

The structure of KEAP1 Kelch Domain Bound to A Small Molecule Fragment also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Chlorine atom in the KEAP1 Kelch Domain Bound to A Small Molecule Fragment (pdb code 7ofa). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the KEAP1 Kelch Domain Bound to A Small Molecule Fragment, PDB code: 7ofa:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the KEAP1 Kelch Domain Bound to A Small Molecule Fragment


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of KEAP1 Kelch Domain Bound to A Small Molecule Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl701 b:44.6 occ:0.87 CL1 A:VBT701 0.0 44.6 0.9 C6 A:VBT701 1.7 41.5 1.0 N1 A:VBT701 2.6 39.3 1.0 C2 A:VBT701 2.7 43.0 1.0 O1 A:VBT701 2.8 42.4 1.0 HG13 A:ILE461 2.8 47.0 1.0 HG A:SER508 2.9 50.5 1.0 HD11 A:ILE461 3.0 58.7 1.0 C1 A:VBT701 3.1 47.6 0.5 HB3 A:PHE478 3.2 50.0 1.0 OG A:SER508 3.4 42.0 1.0 HB2 A:PHE478 3.5 50.0 1.0 HH21 A:ARG415 3.5 71.9 1.0 CG1 A:ILE461 3.6 39.0 1.0 CD1 A:ILE461 3.6 48.8 1.0 NH2 A:ARG415 3.7 59.8 1.0 HD12 A:ILE461 3.7 58.7 1.0 CB A:PHE478 3.7 41.6 1.0 C5 A:VBT701 3.8 39.5 0.9 HA3 A:GLY462 3.8 47.5 1.0 HG12 A:ILE461 3.9 47.0 1.0 HH22 A:ARG415 3.9 71.9 1.0 HD2 A:PHE478 4.0 64.7 1.0 HG2 A:ARG415 4.0 50.6 1.0 C3 A:VBT701 4.0 42.3 1.0 CZ A:ARG415 4.0 63.8 1.0 HE A:ARG415 4.1 73.9 1.0 NE A:ARG415 4.2 61.4 1.0 O2 A:VBT701 4.2 57.3 0.9 CG A:PHE478 4.3 53.3 1.0 CD2 A:PHE478 4.3 53.8 1.0 O A:ILE461 4.4 33.7 1.0 C4 A:VBT701 4.4 40.9 0.6 HD13 A:ILE461 4.5 58.7 1.0 C A:ILE461 4.5 29.1 1.0 N A:GLY462 4.5 34.9 1.0 CA A:GLY462 4.6 39.4 1.0 CB A:SER508 4.7 42.3 1.0 HB3 A:SER508 4.7 50.9 1.0 NH1 A:ARG415 4.7 50.0 1.0 H1 A:VBT701 4.8 50.9 1.0 CB A:ILE461 4.8 34.0 1.0 H A:GLY462 4.9 42.0 1.0 HB A:ILE461 4.9 41.0 1.0 CG A:ARG415 4.9 42.0 1.0 HE A:ARG483 4.9 83.0 1.0 HH12 A:ARG415 4.9 60.2 1.0 HA2 A:GLY462 5.0 47.5 1.0

Chlorine binding site 2 out of 2 in the KEAP1 Kelch Domain Bound to A Small Molecule Fragment


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of KEAP1 Kelch Domain Bound to A Small Molecule Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl701 b:65.0 occ:0.74 CL2 A:VBT701 0.0 65.0 0.7 C5 A:VBT701 1.7 39.5 0.9 N1 A:VBT701 2.6 39.3 1.0 C4 A:VBT701 2.7 40.9 0.6 F1 A:VBT701 3.0 38.4 1.0 HA3 A:GLY509 3.1 45.5 1.0 HG3 A:ARG415 3.1 50.6 1.0 HG2 A:ARG415 3.1 50.6 1.0 HA2 A:GLY509 3.2 45.5 1.0 HB2 A:ALA556 3.3 42.7 1.0 HA A:ALA556 3.4 44.5 1.0 HA2 A:GLY462 3.5 47.5 1.0 CG A:ARG415 3.6 42.0 1.0 CA A:GLY509 3.6 37.8 1.0 C6 A:VBT701 3.9 41.5 1.0 HA3 A:GLY462 3.9 47.5 1.0 HE A:ARG415 3.9 73.9 1.0 CB A:ALA556 3.9 35.5 1.0 C3 A:VBT701 4.0 42.3 1.0 HB1 A:ALA556 4.0 42.7 1.0 CA A:ALA556 4.1 36.9 1.0 CA A:GLY462 4.2 39.4 1.0 H A:ALA556 4.2 43.0 1.0 HD2 A:ARG415 4.4 53.5 1.0 CD A:ARG415 4.4 44.5 1.0 NE A:ARG415 4.4 61.4 1.0 C2 A:VBT701 4.5 43.0 1.0 N A:GLY509 4.5 34.3 1.0 N A:ALA556 4.5 35.7 1.0 H A:GLY509 4.7 41.3 1.0 C A:GLY509 4.7 29.8 1.0 HB3 A:ARG415 4.7 40.1 1.0 H1 A:VBT701 4.7 50.9 1.0 CB A:ARG415 4.8 33.3 1.0 O A:GLY509 4.8 35.4 1.0 HB3 A:ALA556 4.8 42.7 1.0 HA A:ARG415 4.8 36.7 1.0

D.Narayanan, K.T.Tran, J.S.Pallesen, S.M.O.Solbak, Y.Qin, E.Mukminova, M.Luchini, K.O.Vasilyeva, D.Gonzalez Chichon, G.Goutsiou, C.Poulsen, N.Haapanen, G.M.Popowicz, M.Sattler, D.Olagnier, M.Gajhede, A.Bach. Development of Noncovalent Small-Molecule KEAP1-NRF2 Inhibitors By Fragment-Based Drug Discovery. J.Med.Chem. V. 65 14481 2022.
ISSN: ISSN 0022-2623
PubMed: 36263945
DOI: 10.1021/ACS.JMEDCHEM.2C00830