Chlorine in PDB 5qd5: Crystal Structure of Bace Complex with BMC009

All present enzymatic activity of Crystal Structure of Bace Complex with BMC009:
3.4.23.46;

The structure of Crystal Structure of Bace Complex with BMC009, PDB code: 5qd5 was solved by J.M.Rondeau, C.Shao, H.Yang, S.K.Burley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.25 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.013, 103.309, 99.795, 90.00, 104.18, 90.00
R / Rfree (%)	17.7 / 20.7

The binding sites of Chlorine atom in the Crystal Structure of Bace Complex with BMC009 (pdb code 5qd5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Bace Complex with BMC009, PDB code: 5qd5:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Bace Complex with BMC009


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Bace Complex with BMC009 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:53.8 occ:1.00 CL1 A:E6P401 0.0 53.8 1.0 C2 A:E6P401 1.7 39.5 1.0 N3 A:E6P401 2.6 33.8 1.0 C8 A:E6P401 2.7 37.9 1.0 O A:HOH559 3.6 33.8 1.0 NE A:ARG235 3.6 41.6 1.0 NE2 A:GLN73 3.8 67.7 1.0 CD A:ARG235 3.9 35.8 1.0 C4 A:E6P401 3.9 36.9 1.0 CD A:GLN73 3.9 69.5 1.0 C7 A:E6P401 4.0 32.0 1.0 CG A:GLN73 4.0 65.5 1.0 CZ A:ARG235 4.1 46.7 1.0 CG2 A:THR72 4.2 40.2 1.0 C5 A:E6P401 4.4 31.4 1.0 OE1 A:GLN73 4.5 69.2 1.0 NH2 A:ARG235 4.5 47.7 1.0 CG2 A:THR231 4.5 32.5 1.0 O A:HOH597 4.7 43.3 1.0 NH1 A:ARG235 4.8 52.3 1.0 N39 A:E6P401 4.9 35.3 1.0 CB A:GLN73 4.9 63.1 1.0 CB A:THR72 5.0 36.9 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Bace Complex with BMC009


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Bace Complex with BMC009 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:55.8 occ:1.00 CL1 B:E6P401 0.0 55.8 1.0 C2 B:E6P401 1.7 36.5 1.0 N3 B:E6P401 2.6 31.1 1.0 C8 B:E6P401 2.7 31.8 1.0 NE B:ARG235 3.5 43.3 1.0 O B:HOH571 3.6 44.8 1.0 C4 B:E6P401 3.9 37.0 1.0 NE2 B:GLN73 3.9 75.8 1.0 CD B:ARG235 3.9 40.1 1.0 CD B:GLN73 3.9 78.0 1.0 C7 B:E6P401 4.0 38.1 1.0 CG2 B:THR72 4.1 35.2 1.0 CG B:GLN73 4.1 76.6 1.0 CZ B:ARG235 4.1 44.3 1.0 OE1 B:GLN73 4.4 77.9 1.0 NH2 B:ARG235 4.4 40.9 1.0 C5 B:E6P401 4.4 36.1 1.0 O B:HOH590 4.5 48.1 1.0 CG2 B:THR231 4.6 27.7 1.0 NH1 B:ARG235 4.9 50.0 1.0 CB B:GLN73 4.9 68.9 1.0 N39 B:E6P401 4.9 36.3 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Bace Complex with BMC009


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Bace Complex with BMC009 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl401 b:53.7 occ:1.00 CL1 C:E6P401 0.0 53.7 1.0 C2 C:E6P401 1.7 36.3 1.0 N3 C:E6P401 2.6 36.3 1.0 C8 C:E6P401 2.7 27.8 1.0 NE C:ARG235 3.5 45.2 1.0 NE2 C:GLN73 3.7 66.9 1.0 O C:HOH576 3.7 38.2 1.0 C4 C:E6P401 3.9 37.2 1.0 CD C:GLN73 3.9 64.3 1.0 CD C:ARG235 4.0 41.2 1.0 CG2 C:THR72 4.0 35.3 1.0 C7 C:E6P401 4.0 31.0 1.0 CZ C:ARG235 4.0 48.8 1.0 CG C:GLN73 4.2 68.4 1.0 NH2 C:ARG235 4.2 44.1 1.0 C5 C:E6P401 4.5 30.9 1.0 OE1 C:GLN73 4.5 58.9 1.0 O C:HOH541 4.6 48.2 1.0 CG2 C:THR231 4.7 33.8 1.0 NH1 C:ARG235 4.8 57.3 1.0 CB C:THR72 4.9 38.9 1.0 N39 C:E6P401 4.9 43.0 1.0

C.D.Parks, Z.Gaieb, M.Chiu, H.Yang, C.Shao, W.P.Walters, J.M.Jansen, G.Mcgaughey, R.A.Lewis, S.D.Bembenek, M.K.Ameriks, T.Mirzadegan, S.K.Burley, R.E.Amaro, M.K.Gilson. D3R Grand Challenge 4: Blind Prediction of Protein-Ligand Poses, Affinity Rankings, and Relative Binding Free Energies. J.Comput.Aided Mol.Des. V. 34 99 2020.
ISSN: ESSN 1573-4951
PubMed: 31974851
DOI: 10.1007/S10822-020-00289-Y