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Fluorine in PDB 3ohh: Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with Bms-681889 Aka N~1~-Butyl-5-Cyano- N~3~-((1S,2R)-1-(3,5- Difluorobenzyl)-2-Hydroxy-3-((3- Methoxybenzyl)Amino)Propyl)-N~1~- Methyl-1H-Indole-1,3- Dicarboxamide

Enzymatic activity of Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with Bms-681889 Aka N~1~-Butyl-5-Cyano- N~3~-((1S,2R)-1-(3,5- Difluorobenzyl)-2-Hydroxy-3-((3- Methoxybenzyl)Amino)Propyl)-N~1~- Methyl-1H-Indole-1,3- Dicarboxamide

All present enzymatic activity of Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with Bms-681889 Aka N~1~-Butyl-5-Cyano- N~3~-((1S,2R)-1-(3,5- Difluorobenzyl)-2-Hydroxy-3-((3- Methoxybenzyl)Amino)Propyl)-N~1~- Methyl-1H-Indole-1,3- Dicarboxamide:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with Bms-681889 Aka N~1~-Butyl-5-Cyano- N~3~-((1S,2R)-1-(3,5- Difluorobenzyl)-2-Hydroxy-3-((3- Methoxybenzyl)Amino)Propyl)-N~1~- Methyl-1H-Indole-1,3- Dicarboxamide, PDB code: 3ohh 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) 50.00 / 2.01
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 92.177, 86.551, 130.448, 90.00, 100.45, 90.00
R / Rfree (%) 17.1 / 21.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with Bms-681889 Aka N~1~-Butyl-5-Cyano- N~3~-((1S,2R)-1-(3,5- Difluorobenzyl)-2-Hydroxy-3-((3- Methoxybenzyl)Amino)Propyl)-N~1~- Methyl-1H-Indole-1,3- Dicarboxamide (pdb code 3ohh). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with Bms-681889 Aka N~1~-Butyl-5-Cyano- N~3~-((1S,2R)-1-(3,5- Difluorobenzyl)-2-Hydroxy-3-((3- Methoxybenzyl)Amino)Propyl)-N~1~- Methyl-1H-Indole-1,3- Dicarboxamide, PDB code: 3ohh:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 3ohh

Go back to Fluorine Binding Sites List in 3ohh
Fluorine binding site 1 out of 4 in the Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with Bms-681889 Aka N~1~-Butyl-5-Cyano- N~3~-((1S,2R)-1-(3,5- Difluorobenzyl)-2-Hydroxy-3-((3- Methoxybenzyl)Amino)Propyl)-N~1~- Methyl-1H-Indole-1,3- Dicarboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with Bms-681889 Aka N~1~-Butyl-5-Cyano- N~3~-((1S,2R)-1-(3,5- Difluorobenzyl)-2-Hydroxy-3-((3- Methoxybenzyl)Amino)Propyl)-N~1~- Methyl-1H-Indole-1,3- Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:26.8
occ:1.00
 F1 A:3HH501 0.0 26.8 1.0
C56 A:3HH501 1.3 25.3 1.0
C55 A:3HH501 2.4 25.7 1.0
C57 A:3HH501 2.4 25.5 1.0
CD1 A:PHE156 3.4 29.3 1.0
CA A:GLY122 3.6 31.5 1.0
O A:HOH781 3.6 30.1 1.0
C54 A:3HH501 3.6 25.9 1.0
C50 A:3HH501 3.6 25.0 1.0
O A:LYS155 3.6 31.7 1.0
CA A:PHE156 3.8 30.0 1.0
CD2 A:TYR119 3.9 26.7 1.0
N A:GLY122 4.0 31.9 1.0
C A:GLY122 4.0 31.4 1.0
O A:HOH736 4.0 33.2 1.0
O A:HOH873 4.1 37.8 1.0
C53 A:3HH501 4.1 25.7 1.0
CE1 A:PHE156 4.2 29.5 1.0
O A:PHE156 4.2 29.6 1.0
CG A:PHE156 4.3 29.4 1.0
CB A:PHE156 4.3 29.8 1.0
O A:GLY122 4.3 31.3 1.0
CG A:TYR119 4.4 27.6 1.0
CB A:TYR119 4.5 28.6 1.0
C A:LYS155 4.5 31.7 1.0
C A:PHE156 4.5 29.8 1.0
CE2 A:TYR119 4.5 26.5 1.0
N A:PHE156 4.6 30.7 1.0
N A:LYS123 4.6 31.3 1.0
F2 A:3HH501 4.7 26.1 1.0
C48 A:3HH501 4.9 25.4 1.0

Fluorine binding site 2 out of 4 in 3ohh

Go back to Fluorine Binding Sites List in 3ohh
Fluorine binding site 2 out of 4 in the Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with Bms-681889 Aka N~1~-Butyl-5-Cyano- N~3~-((1S,2R)-1-(3,5- Difluorobenzyl)-2-Hydroxy-3-((3- Methoxybenzyl)Amino)Propyl)-N~1~- Methyl-1H-Indole-1,3- Dicarboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with Bms-681889 Aka N~1~-Butyl-5-Cyano- N~3~-((1S,2R)-1-(3,5- Difluorobenzyl)-2-Hydroxy-3-((3- Methoxybenzyl)Amino)Propyl)-N~1~- Methyl-1H-Indole-1,3- Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:26.1
occ:1.00
 F2 A:3HH501 0.0 26.1 1.0
C54 A:3HH501 1.3 25.9 1.0
C55 A:3HH501 2.3 25.7 1.0
C53 A:3HH501 2.4 25.7 1.0
CZ2 A:TRP163 3.4 24.2 1.0
C13 A:3HH501 3.6 25.8 1.0
C56 A:3HH501 3.6 25.3 1.0
CD1 A:ILE158 3.6 29.4 1.0
C50 A:3HH501 3.6 25.0 1.0
C18 A:3HH501 3.7 26.3 1.0
CH2 A:TRP163 3.7 24.9 1.0
CD2 A:LEU78 3.7 21.4 1.0
C15 A:3HH501 3.7 25.7 1.0
C57 A:3HH501 4.1 25.5 1.0
N12 A:3HH501 4.3 26.3 1.0
O A:HOH736 4.3 33.2 1.0
O A:PHE156 4.4 29.6 1.0
C14 A:3HH501 4.5 25.2 1.0
CG1 A:ILE158 4.5 29.4 1.0
O A:GLY278 4.5 21.3 1.0
CE2 A:TRP163 4.6 24.6 1.0
F1 A:3HH501 4.7 26.8 1.0
C2 A:3HH501 4.8 25.8 1.0
C48 A:3HH501 4.9 25.4 1.0
O A:GLN60 5.0 23.4 1.0
C8 A:3HH501 5.0 27.0 1.0
CG A:LEU78 5.0 21.7 1.0
CZ3 A:TRP163 5.0 25.1 1.0

Fluorine binding site 3 out of 4 in 3ohh

Go back to Fluorine Binding Sites List in 3ohh
Fluorine binding site 3 out of 4 in the Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with Bms-681889 Aka N~1~-Butyl-5-Cyano- N~3~-((1S,2R)-1-(3,5- Difluorobenzyl)-2-Hydroxy-3-((3- Methoxybenzyl)Amino)Propyl)-N~1~- Methyl-1H-Indole-1,3- Dicarboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with Bms-681889 Aka N~1~-Butyl-5-Cyano- N~3~-((1S,2R)-1-(3,5- Difluorobenzyl)-2-Hydroxy-3-((3- Methoxybenzyl)Amino)Propyl)-N~1~- Methyl-1H-Indole-1,3- Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:20.3
occ:1.00
 F1 B:3HH501 0.0 20.3 1.0
C56 B:3HH501 1.3 18.4 1.0
C55 B:3HH501 2.3 18.1 1.0
C57 B:3HH501 2.4 17.6 1.0
O B:HOH1020 3.1 42.7 1.0
CD1 B:PHE156 3.2 19.3 1.0
CA B:GLY122 3.5 24.8 1.0
O B:HOH1019 3.5 24.1 1.0
C54 B:3HH501 3.6 18.1 1.0
O B:LYS155 3.6 22.1 1.0
C50 B:3HH501 3.7 18.1 1.0
CA B:PHE156 3.7 19.8 1.0
CD2 B:TYR119 3.8 19.8 1.0
C B:GLY122 3.9 23.8 1.0
N B:GLY122 4.0 26.4 1.0
CE1 B:PHE156 4.0 19.8 1.0
CG B:PHE156 4.1 19.1 1.0
O B:HOH767 4.1 22.6 1.0
CB B:PHE156 4.1 19.6 1.0
C53 B:3HH501 4.1 17.8 1.0
O B:PHE156 4.3 19.0 1.0
CG B:TYR119 4.3 21.2 1.0
CE2 B:TYR119 4.4 21.5 1.0
O B:GLY122 4.4 23.0 1.0
N B:LYS123 4.4 23.0 1.0
CB B:TYR119 4.5 22.4 1.0
C B:LYS155 4.5 22.1 1.0
C B:PHE156 4.5 19.1 1.0
N B:PHE156 4.6 21.0 1.0
F2 B:3HH501 4.7 17.1 1.0
C48 B:3HH501 5.0 18.1 1.0

Fluorine binding site 4 out of 4 in 3ohh

Go back to Fluorine Binding Sites List in 3ohh
Fluorine binding site 4 out of 4 in the Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with Bms-681889 Aka N~1~-Butyl-5-Cyano- N~3~-((1S,2R)-1-(3,5- Difluorobenzyl)-2-Hydroxy-3-((3- Methoxybenzyl)Amino)Propyl)-N~1~- Methyl-1H-Indole-1,3- Dicarboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Beta-Site App-Cleaving Enzyme 1 (Bace-Wt) Complex with Bms-681889 Aka N~1~-Butyl-5-Cyano- N~3~-((1S,2R)-1-(3,5- Difluorobenzyl)-2-Hydroxy-3-((3- Methoxybenzyl)Amino)Propyl)-N~1~- Methyl-1H-Indole-1,3- Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:17.1
occ:1.00
 F2 B:3HH501 0.0 17.1 1.0
C54 B:3HH501 1.3 18.1 1.0
C55 B:3HH501 2.3 18.1 1.0
C53 B:3HH501 2.4 17.8 1.0
CZ2 B:TRP163 3.3 15.7 1.0
CH2 B:TRP163 3.5 15.7 1.0
C56 B:3HH501 3.6 18.4 1.0
CD2 B:LEU78 3.6 15.1 1.0
C50 B:3HH501 3.6 18.1 1.0
CD1 B:ILE158 3.7 19.1 1.0
C13 B:3HH501 3.7 18.3 1.0
C15 B:3HH501 4.0 20.6 1.0
C57 B:3HH501 4.1 17.6 1.0
O B:PHE156 4.2 19.0 1.0
O B:HOH767 4.3 22.6 1.0
C8 B:3HH501 4.3 21.6 1.0
N12 B:3HH501 4.5 18.8 1.0
CE2 B:TRP163 4.5 16.1 1.0
CG1 B:ILE158 4.5 18.7 1.0
C18 B:3HH501 4.5 22.2 1.0
O B:GLY278 4.6 13.9 1.0
F1 B:3HH501 4.7 20.3 1.0
C14 B:3HH501 4.7 19.0 1.0
C48 B:3HH501 4.9 18.1 1.0
CZ3 B:TRP163 4.9 15.9 1.0
CG B:LEU78 4.9 14.7 1.0
C2 B:3HH501 4.9 17.5 1.0
CD1 B:LEU78 5.0 13.7 1.0

Reference:

L.R.Marcin, M.A.Higgins, F.C.Zusi, Y.Zhang, M.F.Dee, M.F.Parker, J.K.Muckelbauer, D.M.Camac, P.E.Morin, V.Ramamurthy, A.J.Tebben, K.A.Lentz, J.E.Grace, J.A.Marcinkeviciene, L.M.Kopcho, C.R.Burton, D.M.Barten, J.H.Toyn, J.E.Meredith, C.F.Albright, J.J.Bronson, J.E.Macor, L.A.Thompson. Synthesis and Sar of Indole-and 7-Azaindole-1,3-Dicarboxamide Hydroxyethylamine Inhibitors of Bace-1. Bioorg.Med.Chem.Lett. V. 21 537 2011.
ISSN: ISSN 0960-894X
PubMed: 21078556
DOI: 10.1016/J.BMCL.2010.10.079
Page generated: Wed Jul 31 21:15:26 2024

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