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Chlorine in PDB 3ckp: Crystal Structure of Bace-1 in Complex with Inhibitor

Enzymatic activity of Crystal Structure of Bace-1 in Complex with Inhibitor

All present enzymatic activity of Crystal Structure of Bace-1 in Complex with Inhibitor:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of Bace-1 in Complex with Inhibitor, PDB code: 3ckp was solved by K.Min, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 224.064, 105.654, 63.700, 90.00, 101.47, 90.00
R / Rfree (%) 24.5 / 30.4

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Bace-1 in Complex with Inhibitor (pdb code 3ckp). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Crystal Structure of Bace-1 in Complex with Inhibitor, PDB code: 3ckp:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 3ckp

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Chlorine binding site 1 out of 9 in the Crystal Structure of Bace-1 in Complex with Inhibitor


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-1 in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:12.1
occ:1.00
 N A:GLU1 3.7 34.2 1.0
CA A:PHE-2 3.7 32.5 1.0
CB A:GLU1 3.8 34.6 1.0
C A:PHE-2 3.8 32.6 1.0
CB A:PHE-2 3.9 30.6 1.0
OE2 A:GLU1 4.0 30.0 1.0
CE A:MET2 4.0 33.2 1.0
O A:PHE-2 4.1 30.5 1.0
N A:VAL-1 4.1 32.4 1.0
CD2 A:PHE-2 4.2 28.9 1.0
CG A:MET2 4.2 33.1 1.0
CA A:GLU1 4.2 34.7 1.0
N A:MET2 4.3 37.0 1.0
CE A:LYS-5 4.4 46.6 1.0
CG A:PHE-2 4.5 29.6 1.0
CD A:GLU1 4.6 33.6 1.0
CG A:GLU1 4.7 34.7 1.0
C A:GLU1 4.7 36.8 1.0
C A:VAL-1 4.7 33.7 1.0
CA A:VAL-1 4.9 34.6 1.0
CB A:MET2 4.9 35.0 1.0
SD A:MET2 5.0 34.4 1.0

Chlorine binding site 2 out of 9 in 3ckp

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Chlorine binding site 2 out of 9 in the Crystal Structure of Bace-1 in Complex with Inhibitor


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-1 in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl603

b:21.1
occ:1.00
 CA A:GLY-4 3.9 36.7 1.0
C A:GLY-4 3.9 35.7 1.0
N A:GLY-4 4.1 39.9 1.0
N A:SER-3 4.1 34.7 1.0
CB A:SER-3 4.3 32.5 1.0
O A:GLY-4 4.4 35.1 1.0
CA A:SER-3 4.8 33.6 1.0

Chlorine binding site 3 out of 9 in 3ckp

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Chlorine binding site 3 out of 9 in the Crystal Structure of Bace-1 in Complex with Inhibitor


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-1 in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl605

b:32.7
occ:1.00
 CD A:LYS65 4.0 45.1 1.0
N C:GLY-4 4.1 47.9 1.0
C C:GLY-4 4.2 43.2 1.0
CA C:GLY-4 4.2 44.0 1.0
N C:SER-3 4.3 40.3 1.0
CB C:SER-3 4.3 32.9 1.0
CD2 A:LEU63 4.5 32.4 1.0
CD1 A:LEU63 4.5 30.2 1.0
NZ A:LYS65 4.6 49.8 1.0
CD1 A:LEU80 4.6 32.9 1.0
O C:GLY-4 4.6 44.3 1.0
CD1 A:LEU133 4.7 33.0 1.0
CG A:LEU63 4.9 33.2 1.0
CA C:SER-3 4.9 37.0 1.0
C C:LYS-5 4.9 50.0 1.0
CE A:LYS65 4.9 47.1 1.0
CB A:LEU63 4.9 32.7 1.0
CB A:LYS65 5.0 43.1 1.0

Chlorine binding site 4 out of 9 in 3ckp

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Chlorine binding site 4 out of 9 in the Crystal Structure of Bace-1 in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Bace-1 in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl607

b:34.9
occ:1.00
 CD A:LYS75 3.1 55.2 1.0
OE1 A:GLU77 3.4 51.1 1.0
CA A:SER105 3.7 50.1 1.0
CG A:GLU77 3.8 48.3 1.0
C A:SER105 3.9 51.7 1.0
O A:GLU104 3.9 45.0 1.0
N A:SER105 4.0 47.8 1.0
N A:ASP106 4.0 52.6 1.0
CG A:LYS75 4.0 49.2 1.0
CD A:GLU77 4.0 50.8 1.0
C A:GLU104 4.1 46.1 1.0
O A:LYS75 4.1 39.7 1.0
NZ A:LYS75 4.3 59.0 1.0
CB A:ASP106 4.3 56.6 1.0
CE A:LYS75 4.3 57.0 1.0
CA A:TRP76 4.4 36.9 1.0
C A:LYS75 4.4 40.0 1.0
C A:TRP76 4.4 37.7 1.0
N A:GLU77 4.5 40.2 1.0
O A:SER105 4.5 52.4 1.0
CB A:GLU77 4.5 44.5 1.0
CB A:GLU104 4.5 47.3 1.0
N A:TRP76 4.6 37.8 1.0
CA A:ASP106 4.8 53.0 1.0
CB A:LYS75 4.8 44.6 1.0
OE1 A:GLU104 4.9 57.8 1.0
O A:TRP76 5.0 36.5 1.0
CA A:GLU104 5.0 45.4 1.0

Chlorine binding site 5 out of 9 in 3ckp

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Chlorine binding site 5 out of 9 in the Crystal Structure of Bace-1 in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Bace-1 in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl608

b:39.8
occ:1.00
 O A:HOH631 3.4 29.5 1.0
N A:ASN278 3.5 30.5 1.0
ND2 A:ASN278 3.5 32.5 1.0
CB A:ASN278 3.8 32.1 1.0
CB A:TRP277 3.9 29.0 1.0
N A:TRP277 4.0 31.4 1.0
CG A:ASN278 4.2 35.3 1.0
CA A:ASN278 4.3 32.4 1.0
CA A:TRP277 4.3 31.2 1.0
CD1 A:TRP277 4.3 29.3 1.0
C A:TRP277 4.4 30.9 1.0
CG A:TRP277 4.5 30.2 1.0
O A:THR275 4.5 38.1 1.0
OD2 A:ASP363 4.6 51.3 1.0
CD1 A:PHE365 4.6 34.2 1.0
CE1 A:PHE365 4.7 33.3 1.0
C A:PRO276 4.7 33.2 1.0
CG A:ASP363 4.8 48.9 1.0

Chlorine binding site 6 out of 9 in 3ckp

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Chlorine binding site 6 out of 9 in the Crystal Structure of Bace-1 in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Bace-1 in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl602

b:23.4
occ:1.00
 O B:GLU104 4.0 53.8 1.0
O B:LYS75 4.0 43.9 1.0
CG B:LYS75 4.1 39.0 1.0
N B:GLU77 4.2 43.0 1.0
C B:GLU104 4.2 54.0 1.0
CA B:TRP76 4.2 40.5 1.0
C B:TRP76 4.2 40.9 1.0
N B:ASP106 4.2 54.7 1.0
CA B:SER105 4.3 53.4 1.0
CB B:GLU77 4.3 48.1 1.0
N B:SER105 4.3 53.0 1.0
CB B:GLU104 4.4 57.8 1.0
C B:LYS75 4.4 42.5 1.0
C B:SER105 4.5 54.0 1.0
CB B:ASP106 4.5 55.5 1.0
N B:TRP76 4.5 41.0 1.0
CE B:LYS75 4.6 44.1 1.0
NZ B:LYS75 4.6 44.8 1.0
OE1 B:GLU77 4.6 63.3 1.0
O B:TRP76 4.8 40.2 1.0
CE1 B:TYR68 4.8 59.4 1.0
CA B:GLU77 4.9 44.9 1.0
CD B:LYS75 4.9 41.5 1.0
OE1 B:GLU104 5.0 70.2 1.0
CA B:GLU104 5.0 54.6 1.0

Chlorine binding site 7 out of 9 in 3ckp

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Chlorine binding site 7 out of 9 in the Crystal Structure of Bace-1 in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Bace-1 in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl606

b:36.9
occ:1.00
 N B:TYR68 3.5 43.1 1.0
CB B:PRO129 3.7 37.4 1.0
O B:TYR68 3.8 45.9 1.0
CA B:PRO129 3.8 37.6 1.0
CG B:PRO129 3.9 38.7 1.0
CB B:TYR68 3.9 50.5 1.0
CA B:TYR68 4.2 46.6 1.0
CA B:VAL67 4.4 38.9 1.0
C B:VAL67 4.4 40.8 1.0
CB B:ARG128 4.5 40.5 1.0
C B:TYR68 4.5 45.7 1.0
N B:PRO129 4.6 37.2 1.0
O B:GLY66 4.7 39.8 1.0
CD B:PRO129 4.9 39.8 1.0
C B:PRO129 4.9 36.0 1.0
CG2 B:VAL67 4.9 34.9 1.0
O B:PRO129 5.0 38.9 1.0

Chlorine binding site 8 out of 9 in 3ckp

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Chlorine binding site 8 out of 9 in the Crystal Structure of Bace-1 in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Bace-1 in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl604

b:32.6
occ:1.00
 CG C:GLU1 3.4 40.0 1.0
CE C:MET2 3.5 37.1 1.0
CB C:GLU1 3.6 40.1 1.0
CB C:PHE-2 3.9 35.0 1.0
CA C:PHE-2 3.9 36.5 1.0
N C:GLU1 4.0 38.7 1.0
CD2 C:PHE-2 4.0 32.6 1.0
C C:PHE-2 4.1 36.2 1.0
CA C:GLU1 4.3 37.0 1.0
N C:MET2 4.4 36.1 1.0
O C:PHE-2 4.4 36.1 1.0
CG C:PHE-2 4.4 33.5 1.0
N C:VAL-1 4.5 36.0 1.0
CG C:MET2 4.6 37.0 1.0
CD C:GLU1 4.7 39.7 1.0
C C:GLU1 4.8 36.6 1.0
SD C:MET2 4.9 42.2 1.0
NZ C:LYS-5 5.0 41.9 1.0
CB C:MET2 5.0 37.1 1.0

Chlorine binding site 9 out of 9 in 3ckp

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Chlorine binding site 9 out of 9 in the Crystal Structure of Bace-1 in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Bace-1 in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl609

b:43.2
occ:1.00
 OE2 C:GLU77 3.4 68.9 1.0
N C:ASP106 3.9 66.5 1.0
CA C:SER105 3.9 67.0 1.0
O C:GLU104 3.9 66.2 1.0
C C:SER105 3.9 66.7 1.0
N C:SER105 4.0 66.7 1.0
C C:GLU104 4.0 66.1 1.0
CD C:LYS75 4.1 59.0 1.0
CB C:GLU77 4.1 62.7 1.0
CB C:ASP106 4.1 66.8 1.0
CB C:GLU104 4.3 69.4 1.0
O C:LYS75 4.4 56.4 1.0
N C:GLU77 4.4 58.8 1.0
C C:TRP76 4.4 56.8 1.0
CG C:LYS75 4.5 58.0 1.0
CD C:GLU77 4.5 69.0 1.0
CA C:TRP76 4.5 55.2 1.0
O C:SER105 4.6 65.7 1.0
CA C:ASP106 4.6 66.5 1.0
C C:LYS75 4.8 56.9 1.0
CA C:GLU104 4.9 66.5 1.0
CA C:GLU77 4.9 60.6 1.0
N C:TRP76 4.9 55.6 1.0
O C:TRP76 4.9 57.2 1.0
CG C:GLU77 5.0 66.6 1.0

Reference:

H.Park, K.Min, H.-S.Kwak, K.D.Koo, D.Lim, S.-W.Seo, J.-U.Choi, B.Platt, D.-Y.Choi. Synthesis, Sar, and X-Ray Structure of Human Bace-1 Inhibitors with Cyclic Urea Derivatives Bioorg.Med.Chem.Lett. V. 18 2900 2008.
ISSN: ISSN 0960-894X
PubMed: 18434152
DOI: 10.1016/J.BMCL.2008.03.081
Page generated: Fri Jul 11 04:05:12 2025

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