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Iodine in PDB 4fse: Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with N-(N-(4-Amino-3,5- Dichlorobenzyl)Carbamimidoyl)-3-(4- Methoxyphenyl)-5- Methyl-4-Isothiazolecarboxamide

Enzymatic activity of Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with N-(N-(4-Amino-3,5- Dichlorobenzyl)Carbamimidoyl)-3-(4- Methoxyphenyl)-5- Methyl-4-Isothiazolecarboxamide

All present enzymatic activity of Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with N-(N-(4-Amino-3,5- Dichlorobenzyl)Carbamimidoyl)-3-(4- Methoxyphenyl)-5- Methyl-4-Isothiazolecarboxamide:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with N-(N-(4-Amino-3,5- Dichlorobenzyl)Carbamimidoyl)-3-(4- Methoxyphenyl)-5- Methyl-4-Isothiazolecarboxamide, PDB code: 4fse was solved by J.K.Muckelbauer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.08 / 2.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.334, 131.219, 88.947, 90.00, 97.60, 90.00
R / Rfree (%) 21.7 / 26.7

Other elements in 4fse:

The structure of Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with N-(N-(4-Amino-3,5- Dichlorobenzyl)Carbamimidoyl)-3-(4- Methoxyphenyl)-5- Methyl-4-Isothiazolecarboxamide also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with N-(N-(4-Amino-3,5- Dichlorobenzyl)Carbamimidoyl)-3-(4- Methoxyphenyl)-5- Methyl-4-Isothiazolecarboxamide (pdb code 4fse). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with N-(N-(4-Amino-3,5- Dichlorobenzyl)Carbamimidoyl)-3-(4- Methoxyphenyl)-5- Methyl-4-Isothiazolecarboxamide, PDB code: 4fse:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 4fse

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Iodine binding site 1 out of 9 in the Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with N-(N-(4-Amino-3,5- Dichlorobenzyl)Carbamimidoyl)-3-(4- Methoxyphenyl)-5- Methyl-4-Isothiazolecarboxamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with N-(N-(4-Amino-3,5- Dichlorobenzyl)Carbamimidoyl)-3-(4- Methoxyphenyl)-5- Methyl-4-Isothiazolecarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:77.6
occ:1.00
N A:ASN281 3.6 13.3 1.0
CB A:ASN281 3.7 12.6 1.0
CG A:ASN281 3.7 11.3 1.0
NH2 A:ARG283 3.8 16.0 1.0
ND2 A:ASN281 3.8 9.6 1.0
CG2 A:THR279 3.9 15.4 1.0
C19 A:0VA501 4.0 35.4 1.0
C04 A:0VA501 4.0 33.8 1.0
O27 A:0VA501 4.1 34.2 1.0
N A:THR280 4.1 14.1 1.0
CB A:THR280 4.2 13.6 1.0
OD1 A:ASN281 4.2 10.9 1.0
CD A:ARG283 4.3 15.8 1.0
CA A:ASN281 4.3 12.9 1.0
C11 A:0VA501 4.3 34.1 1.0
OG A:SER373 4.4 16.1 1.0
CA A:THR280 4.5 13.8 1.0
C A:THR280 4.5 13.6 1.0
CG A:ARG283 4.6 15.1 1.0
OG1 A:THR280 4.8 13.9 1.0
CZ A:ARG283 4.8 16.9 1.0

Iodine binding site 2 out of 9 in 4fse

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Iodine binding site 2 out of 9 in the Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with N-(N-(4-Amino-3,5- Dichlorobenzyl)Carbamimidoyl)-3-(4- Methoxyphenyl)-5- Methyl-4-Isothiazolecarboxamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with N-(N-(4-Amino-3,5- Dichlorobenzyl)Carbamimidoyl)-3-(4- Methoxyphenyl)-5- Methyl-4-Isothiazolecarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I503

b:65.4
occ:1.00
CG A:LYS123 3.9 27.4 1.0
O A:GLU152 4.0 24.5 1.0
CG A:GLU125 4.1 27.0 1.0
C A:GLU152 4.1 24.5 1.0
N A:GLU125 4.2 24.0 1.0
CA A:SER153 4.2 25.1 1.0
CB A:GLU152 4.2 24.6 1.0
CA A:TRP124 4.2 24.4 1.0
C A:TRP124 4.2 24.2 1.0
N A:SER153 4.2 24.9 1.0
O A:LYS123 4.2 26.1 1.0
CD A:LYS123 4.3 28.6 1.0
CE A:LYS123 4.3 29.7 1.0
N A:ASP154 4.4 25.6 1.0
C A:LYS123 4.4 26.3 1.0
OE2 A:GLU125 4.4 31.7 1.0
C A:SER153 4.4 25.3 1.0
N A:TRP124 4.5 25.2 1.0
CB A:GLU125 4.5 24.5 1.0
CE1 A:TYR116 4.6 34.3 1.0
CD A:GLU125 4.6 30.1 1.0
CB A:LYS123 4.7 27.1 1.0
NZ A:LYS123 4.7 29.9 1.0
O A:TRP124 4.8 24.0 1.0
CA A:GLU152 4.9 24.3 1.0
CB A:ASP154 4.9 26.3 1.0
CA A:GLU125 5.0 24.0 1.0

Iodine binding site 3 out of 9 in 4fse

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Iodine binding site 3 out of 9 in the Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with N-(N-(4-Amino-3,5- Dichlorobenzyl)Carbamimidoyl)-3-(4- Methoxyphenyl)-5- Methyl-4-Isothiazolecarboxamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with N-(N-(4-Amino-3,5- Dichlorobenzyl)Carbamimidoyl)-3-(4- Methoxyphenyl)-5- Methyl-4-Isothiazolecarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I502

b:74.6
occ:1.00
N B:ASN281 3.6 13.3 1.0
CG B:ASN281 3.8 10.4 1.0
CB B:ASN281 3.8 12.5 1.0
NH2 B:ARG283 3.8 16.4 1.0
O B:HOH705 3.8 6.8 1.0
ND2 B:ASN281 3.9 9.1 1.0
C04 B:0VA501 4.0 30.3 1.0
C19 B:0VA501 4.0 32.2 1.0
N B:THR280 4.1 14.2 1.0
CB B:THR280 4.1 13.4 1.0
CG2 B:THR279 4.1 14.8 1.0
OD1 B:ASN281 4.2 8.8 1.0
CA B:ASN281 4.3 12.9 1.0
CA B:THR280 4.4 13.8 1.0
CD B:ARG283 4.5 15.6 1.0
O27 B:0VA501 4.5 31.4 1.0
C11 B:0VA501 4.5 30.6 1.0
C B:THR280 4.5 13.6 1.0
OG B:SER373 4.6 17.3 1.0
CG B:ARG283 4.8 14.7 1.0
OG1 B:THR280 4.9 13.3 1.0
CZ B:ARG283 4.9 16.8 1.0
C02 B:0VA501 4.9 31.0 1.0
CG2 B:THR280 4.9 13.3 1.0

Iodine binding site 4 out of 9 in 4fse

Go back to Iodine Binding Sites List in 4fse
Iodine binding site 4 out of 9 in the Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with N-(N-(4-Amino-3,5- Dichlorobenzyl)Carbamimidoyl)-3-(4- Methoxyphenyl)-5- Methyl-4-Isothiazolecarboxamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with N-(N-(4-Amino-3,5- Dichlorobenzyl)Carbamimidoyl)-3-(4- Methoxyphenyl)-5- Methyl-4-Isothiazolecarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I503

b:69.3
occ:1.00
CG B:LYS123 3.8 27.7 1.0
CE B:LYS123 3.9 30.7 1.0
NZ B:LYS123 4.0 30.7 1.0
O B:GLU152 4.1 24.5 1.0
CA B:SER153 4.1 24.9 1.0
C B:GLU152 4.1 24.5 1.0
N B:SER153 4.2 24.7 1.0
O B:LYS123 4.2 26.0 1.0
N B:ASP154 4.2 25.5 1.0
C B:SER153 4.3 25.2 1.0
CA B:TRP124 4.4 24.5 1.0
N B:GLU125 4.4 24.1 1.0
CD B:LYS123 4.4 29.2 1.0
CB B:GLU152 4.4 24.3 1.0
C B:LYS123 4.4 26.2 1.0
C B:TRP124 4.4 24.2 1.0
CB B:ASP154 4.6 26.1 1.0
N B:TRP124 4.6 25.3 1.0
CG B:GLU125 4.6 26.6 1.0
CB B:LYS123 4.7 27.3 1.0
CB B:GLU125 4.8 24.2 1.0
CD B:GLU125 4.9 29.7 1.0
CE1 B:TYR116 4.9 33.9 1.0
O B:SER153 4.9 25.3 1.0
CA B:GLU152 4.9 24.2 1.0

Iodine binding site 5 out of 9 in 4fse

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Iodine binding site 5 out of 9 in the Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with N-(N-(4-Amino-3,5- Dichlorobenzyl)Carbamimidoyl)-3-(4- Methoxyphenyl)-5- Methyl-4-Isothiazolecarboxamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with N-(N-(4-Amino-3,5- Dichlorobenzyl)Carbamimidoyl)-3-(4- Methoxyphenyl)-5- Methyl-4-Isothiazolecarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I502

b:57.0
occ:1.00
N D:ASN281 3.6 13.3 1.0
CB D:ASN281 3.7 12.6 1.0
CG D:ASN281 3.7 11.3 1.0
O D:HOH643 3.8 6.3 1.0
CG2 D:THR279 3.8 14.8 1.0
ND2 D:ASN281 4.0 9.0 1.0
C04 D:0VA501 4.0 29.8 1.0
OD1 D:ASN281 4.0 10.5 1.0
NH2 D:ARG283 4.1 14.5 1.0
N D:THR280 4.1 14.2 1.0
CB D:THR280 4.1 13.8 1.0
CA D:ASN281 4.2 13.0 1.0
CD D:ARG283 4.4 16.1 1.0
CA D:THR280 4.4 13.8 1.0
O27 D:0VA501 4.4 31.1 1.0
C D:THR280 4.5 13.7 1.0
C11 D:0VA501 4.5 30.6 1.0
OG D:SER373 4.7 16.6 1.0
CG D:ARG283 4.7 15.2 1.0
OG1 D:THR280 4.9 13.6 1.0

Iodine binding site 6 out of 9 in 4fse

Go back to Iodine Binding Sites List in 4fse
Iodine binding site 6 out of 9 in the Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with N-(N-(4-Amino-3,5- Dichlorobenzyl)Carbamimidoyl)-3-(4- Methoxyphenyl)-5- Methyl-4-Isothiazolecarboxamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with N-(N-(4-Amino-3,5- Dichlorobenzyl)Carbamimidoyl)-3-(4- Methoxyphenyl)-5- Methyl-4-Isothiazolecarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I503

b:71.7
occ:1.00
O D:GLU152 4.0 24.3 1.0
CG D:LYS123 4.0 27.7 1.0
C D:GLU152 4.0 24.5 1.0
CA D:SER153 4.0 25.0 1.0
N D:SER153 4.1 24.7 1.0
CB D:GLU152 4.1 24.8 1.0
O D:LYS123 4.2 26.0 1.0
CB D:GLU125 4.2 24.4 1.0
N D:ASP154 4.2 25.6 1.0
CA D:TRP124 4.3 24.4 1.0
C D:SER153 4.3 25.2 1.0
CE D:LYS123 4.3 30.6 1.0
C D:TRP124 4.3 24.3 1.0
OE1 D:GLU125 4.3 30.7 1.0
N D:GLU125 4.4 24.2 1.0
C D:LYS123 4.4 26.3 1.0
CD D:LYS123 4.4 29.7 1.0
N D:TRP124 4.5 25.2 1.0
CB D:LYS123 4.6 27.2 1.0
CE1 D:TYR116 4.7 33.8 1.0
CB D:ASP154 4.7 26.1 1.0
NZ D:LYS123 4.7 31.4 1.0
CA D:GLU152 4.8 24.4 1.0
O D:TRP124 4.9 24.1 1.0
O D:SER153 5.0 25.3 1.0
CA D:GLU125 5.0 24.0 1.0

Iodine binding site 7 out of 9 in 4fse

Go back to Iodine Binding Sites List in 4fse
Iodine binding site 7 out of 9 in the Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with N-(N-(4-Amino-3,5- Dichlorobenzyl)Carbamimidoyl)-3-(4- Methoxyphenyl)-5- Methyl-4-Isothiazolecarboxamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with N-(N-(4-Amino-3,5- Dichlorobenzyl)Carbamimidoyl)-3-(4- Methoxyphenyl)-5- Methyl-4-Isothiazolecarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:I502

b:86.0
occ:1.00
N E:ASN281 3.7 13.3 1.0
CB E:ASN281 3.8 12.2 1.0
C19 E:0VA501 3.8 33.8 1.0
CG E:ASN281 3.8 11.2 1.0
NH2 E:ARG283 3.8 16.2 1.0
O27 E:0VA501 3.8 33.0 1.0
O E:HOH664 4.0 17.1 1.0
C04 E:0VA501 4.0 32.2 1.0
ND2 E:ASN281 4.1 9.9 1.0
C11 E:0VA501 4.2 32.7 1.0
CG2 E:THR279 4.2 14.9 1.0
OD1 E:ASN281 4.2 9.4 1.0
N E:THR280 4.2 14.2 1.0
CB E:THR280 4.2 13.7 1.0
OG E:SER373 4.3 16.6 1.0
CA E:ASN281 4.4 12.9 1.0
CD E:ARG283 4.4 16.2 1.0
CA E:THR280 4.6 13.8 1.0
C E:THR280 4.7 13.7 1.0
CG E:ARG283 4.7 15.3 1.0
CZ E:ARG283 4.9 17.6 1.0

Iodine binding site 8 out of 9 in 4fse

Go back to Iodine Binding Sites List in 4fse
Iodine binding site 8 out of 9 in the Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with N-(N-(4-Amino-3,5- Dichlorobenzyl)Carbamimidoyl)-3-(4- Methoxyphenyl)-5- Methyl-4-Isothiazolecarboxamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with N-(N-(4-Amino-3,5- Dichlorobenzyl)Carbamimidoyl)-3-(4- Methoxyphenyl)-5- Methyl-4-Isothiazolecarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:I503

b:70.3
occ:1.00
CG E:LYS123 3.9 27.6 1.0
O E:GLU152 4.0 24.5 1.0
CA E:SER153 4.1 25.0 1.0
C E:GLU152 4.1 24.5 1.0
CD E:LYS123 4.1 28.9 1.0
CB E:GLU125 4.1 24.4 1.0
CE E:LYS123 4.1 30.0 1.0
N E:SER153 4.1 24.8 1.0
O E:LYS123 4.2 26.1 1.0
CA E:TRP124 4.2 24.4 1.0
CB E:GLU152 4.2 24.7 1.0
N E:ASP154 4.2 25.6 1.0
C E:TRP124 4.3 24.2 1.0
OE1 E:GLU125 4.3 30.2 1.0
C E:SER153 4.3 25.2 1.0
N E:GLU125 4.3 24.0 1.0
C E:LYS123 4.4 26.3 1.0
N E:TRP124 4.5 25.3 1.0
CB E:LYS123 4.6 27.3 1.0
CE1 E:TYR116 4.6 34.4 1.0
NZ E:LYS123 4.6 30.8 1.0
CB E:ASP154 4.7 26.1 1.0
O E:TRP124 4.8 24.1 1.0
CA E:GLU152 4.8 24.3 1.0
CA E:GLU125 4.9 24.0 1.0
CD E:GLU125 5.0 30.0 1.0
O E:SER153 5.0 25.1 1.0

Iodine binding site 9 out of 9 in 4fse

Go back to Iodine Binding Sites List in 4fse
Iodine binding site 9 out of 9 in the Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with N-(N-(4-Amino-3,5- Dichlorobenzyl)Carbamimidoyl)-3-(4- Methoxyphenyl)-5- Methyl-4-Isothiazolecarboxamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with N-(N-(4-Amino-3,5- Dichlorobenzyl)Carbamimidoyl)-3-(4- Methoxyphenyl)-5- Methyl-4-Isothiazolecarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:I504

b:0.0
occ:1.00
CG2 E:THR130 4.4 14.7 1.0
ND2 E:ASN146 4.8 17.2 1.0

Reference:

S.W.Gerritz, W.Zhai, S.Shi, S.Zhu, J.H.Toyn, J.E.Meredith, L.G.Iben, C.R.Burton, C.F.Albright, A.C.Good, A.J.Tebben, J.K.Muckelbauer, D.M.Camac, W.Metzler, L.S.Cook, R.Padmanabha, K.A.Lentz, M.J.Sofia, M.A.Poss, J.E.Macor, L.A.Thompson. Acyl Guanidine Inhibitors of Beta-Secretase (Bace-1): Optimization of A Micromolar Hit to A Nanomolar Lead Via Iterative Solid- and Solution-Phase Library Synthesis J.Med.Chem. V. 55 9208 2012.
ISSN: ISSN 0022-2623
PubMed: 23030502
DOI: 10.1021/JM300931Y
Page generated: Sun Dec 13 19:32:43 2020

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