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Fluorine in PDB 2vnm: Human Bace-1 in Complex with 3-(1,1-Dioxidotetrahydro-2H-1,2-Thiazin- 2-Yl)-5-(Ethylamino)-N-((1S,2R)-2-Hydroxy-1-(Phenylmethyl)-3-(((3- (Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)Benzamide

Enzymatic activity of Human Bace-1 in Complex with 3-(1,1-Dioxidotetrahydro-2H-1,2-Thiazin- 2-Yl)-5-(Ethylamino)-N-((1S,2R)-2-Hydroxy-1-(Phenylmethyl)-3-(((3- (Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)Benzamide

All present enzymatic activity of Human Bace-1 in Complex with 3-(1,1-Dioxidotetrahydro-2H-1,2-Thiazin- 2-Yl)-5-(Ethylamino)-N-((1S,2R)-2-Hydroxy-1-(Phenylmethyl)-3-(((3- (Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)Benzamide:
3.4.23.46;

Protein crystallography data

The structure of Human Bace-1 in Complex with 3-(1,1-Dioxidotetrahydro-2H-1,2-Thiazin- 2-Yl)-5-(Ethylamino)-N-((1S,2R)-2-Hydroxy-1-(Phenylmethyl)-3-(((3- (Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)Benzamide, PDB code: 2vnm was solved by N.Charrier, B.Clarke, L.Cutler, E.Demont, C.Dingwall, R.Dunsdon, P.East, J.Hawkins, C.Howes, I.Hussain, P.Jeffrey, G.Maile, R.Matico, J.Mosley, A.Naylor, A.Obrien, S.Redshaw, P.Rowland, V.Soleil, K.J.Smith, S.Sweitzer, P.Theobald, D.Vesey, D.S.Walter, G.Wayne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.55 / 1.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.952, 76.217, 104.492, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 23.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Bace-1 in Complex with 3-(1,1-Dioxidotetrahydro-2H-1,2-Thiazin- 2-Yl)-5-(Ethylamino)-N-((1S,2R)-2-Hydroxy-1-(Phenylmethyl)-3-(((3- (Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)Benzamide (pdb code 2vnm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Human Bace-1 in Complex with 3-(1,1-Dioxidotetrahydro-2H-1,2-Thiazin- 2-Yl)-5-(Ethylamino)-N-((1S,2R)-2-Hydroxy-1-(Phenylmethyl)-3-(((3- (Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)Benzamide, PDB code: 2vnm:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 2vnm

Go back to Fluorine Binding Sites List in 2vnm
Fluorine binding site 1 out of 6 in the Human Bace-1 in Complex with 3-(1,1-Dioxidotetrahydro-2H-1,2-Thiazin- 2-Yl)-5-(Ethylamino)-N-((1S,2R)-2-Hydroxy-1-(Phenylmethyl)-3-(((3- (Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Bace-1 in Complex with 3-(1,1-Dioxidotetrahydro-2H-1,2-Thiazin- 2-Yl)-5-(Ethylamino)-N-((1S,2R)-2-Hydroxy-1-(Phenylmethyl)-3-(((3- (Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2000

b:23.1
occ:1.00
 F44 A:CM82000 0.0 23.1 1.0
C41 A:CM82000 1.4 18.9 1.0
F42 A:CM82000 2.2 21.6 1.0
F43 A:CM82000 2.2 22.1 1.0
C39 A:CM82000 2.4 16.3 1.0
C38 A:CM82000 2.7 15.3 1.0
NH2 A:ARG189 3.7 37.4 1.0
C40 A:CM82000 3.7 14.0 1.0
NE A:ARG189 3.9 32.2 1.0
CG1 A:VAL130 4.0 12.8 1.0
CZ A:ARG189 4.0 35.4 1.0
O A:PRO131 4.1 14.0 1.0
C37 A:CM82000 4.1 15.3 1.0
O A:HOH2033 4.3 12.8 1.0
O A:ILE187 4.6 14.2 1.0
CG A:ARG189 4.7 20.6 1.0
C35 A:CM82000 4.9 14.6 1.0
CD1 A:TYR132 4.9 14.4 1.0
C A:PRO131 4.9 14.1 1.0
CD A:ARG189 4.9 28.5 1.0
OH A:TYR259 5.0 18.8 1.0

Fluorine binding site 2 out of 6 in 2vnm

Go back to Fluorine Binding Sites List in 2vnm
Fluorine binding site 2 out of 6 in the Human Bace-1 in Complex with 3-(1,1-Dioxidotetrahydro-2H-1,2-Thiazin- 2-Yl)-5-(Ethylamino)-N-((1S,2R)-2-Hydroxy-1-(Phenylmethyl)-3-(((3- (Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Bace-1 in Complex with 3-(1,1-Dioxidotetrahydro-2H-1,2-Thiazin- 2-Yl)-5-(Ethylamino)-N-((1S,2R)-2-Hydroxy-1-(Phenylmethyl)-3-(((3- (Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2000

b:22.1
occ:1.00
 F43 A:CM82000 0.0 22.1 1.0
C41 A:CM82000 1.4 18.9 1.0
F42 A:CM82000 2.2 21.6 1.0
F44 A:CM82000 2.2 23.1 1.0
C39 A:CM82000 2.3 16.3 1.0
C40 A:CM82000 3.0 14.0 1.0
CB A:SER96 3.1 10.0 1.0
CE1 A:TYR132 3.4 14.0 1.0
C38 A:CM82000 3.5 15.3 1.0
CD1 A:TYR132 3.5 14.4 1.0
O A:HOH2033 3.6 12.8 1.0
CG1 A:VAL130 3.8 12.8 1.0
CA A:SER96 4.0 10.0 1.0
OG A:SER96 4.2 11.0 1.0
C35 A:CM82000 4.3 14.6 1.0
O A:GLY95 4.3 10.1 1.0
O31 A:CM82000 4.4 12.1 1.0
CZ A:TYR132 4.5 11.8 1.0
C37 A:CM82000 4.7 15.3 1.0
CG A:TYR132 4.7 13.5 1.0
O A:HOH2087 4.8 13.5 1.0
N A:SER97 4.9 9.4 1.0
N A:SER96 5.0 10.1 1.0

Fluorine binding site 3 out of 6 in 2vnm

Go back to Fluorine Binding Sites List in 2vnm
Fluorine binding site 3 out of 6 in the Human Bace-1 in Complex with 3-(1,1-Dioxidotetrahydro-2H-1,2-Thiazin- 2-Yl)-5-(Ethylamino)-N-((1S,2R)-2-Hydroxy-1-(Phenylmethyl)-3-(((3- (Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Bace-1 in Complex with 3-(1,1-Dioxidotetrahydro-2H-1,2-Thiazin- 2-Yl)-5-(Ethylamino)-N-((1S,2R)-2-Hydroxy-1-(Phenylmethyl)-3-(((3- (Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2000

b:21.6
occ:1.00
 F42 A:CM82000 0.0 21.6 1.0
C41 A:CM82000 1.3 18.9 1.0
F44 A:CM82000 2.2 23.1 1.0
F43 A:CM82000 2.2 22.1 1.0
C39 A:CM82000 2.3 16.3 1.0
C40 A:CM82000 2.9 14.0 1.0
C38 A:CM82000 3.4 15.3 1.0
O A:HOH2033 3.7 12.8 1.0
CD1 A:ILE187 3.8 15.4 1.0
OH A:TYR259 3.8 18.8 1.0
O A:ILE187 3.9 14.2 1.0
CB A:SER96 4.1 10.0 1.0
O A:GLY95 4.2 10.1 1.0
CB A:ILE187 4.2 14.4 1.0
CE1 A:TYR259 4.2 13.7 1.0
CA A:SER96 4.2 10.0 1.0
C35 A:CM82000 4.2 14.6 1.0
CZ A:TYR259 4.3 16.5 1.0
CG1 A:ILE187 4.3 12.8 1.0
C37 A:CM82000 4.6 15.3 1.0
C A:ILE187 4.8 13.6 1.0
C36 A:CM82000 4.9 15.8 1.0

Fluorine binding site 4 out of 6 in 2vnm

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Fluorine binding site 4 out of 6 in the Human Bace-1 in Complex with 3-(1,1-Dioxidotetrahydro-2H-1,2-Thiazin- 2-Yl)-5-(Ethylamino)-N-((1S,2R)-2-Hydroxy-1-(Phenylmethyl)-3-(((3- (Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Bace-1 in Complex with 3-(1,1-Dioxidotetrahydro-2H-1,2-Thiazin- 2-Yl)-5-(Ethylamino)-N-((1S,2R)-2-Hydroxy-1-(Phenylmethyl)-3-(((3- (Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:20.0
occ:1.00
 F44 A:CM82001 0.0 20.0 1.0
C41 A:CM82001 1.3 20.0 1.0
F42 A:CM82001 2.1 20.0 1.0
F43 A:CM82001 2.2 20.0 1.0
C39 A:CM82001 2.4 20.0 1.0
C38 A:CM82001 3.0 20.0 1.0
C02 A:CM82001 3.5 20.0 1.0
C40 A:CM82001 3.6 20.0 1.0
CG A:GLN204 3.9 18.5 1.0
C01 A:CM82001 4.0 20.0 1.0
O A:HOH2164 4.1 33.9 1.0
CD A:GLN204 4.3 18.1 1.0
OE1 A:GLN204 4.3 17.1 1.0
C37 A:CM82001 4.4 20.0 1.0
CB A:GLN204 4.4 18.8 1.0
CA A:GLN204 4.8 19.3 1.0
C35 A:CM82001 4.8 20.0 1.0
O A:GLN204 5.0 19.9 1.0

Fluorine binding site 5 out of 6 in 2vnm

Go back to Fluorine Binding Sites List in 2vnm
Fluorine binding site 5 out of 6 in the Human Bace-1 in Complex with 3-(1,1-Dioxidotetrahydro-2H-1,2-Thiazin- 2-Yl)-5-(Ethylamino)-N-((1S,2R)-2-Hydroxy-1-(Phenylmethyl)-3-(((3- (Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human Bace-1 in Complex with 3-(1,1-Dioxidotetrahydro-2H-1,2-Thiazin- 2-Yl)-5-(Ethylamino)-N-((1S,2R)-2-Hydroxy-1-(Phenylmethyl)-3-(((3- (Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:20.0
occ:1.00
 F43 A:CM82001 0.0 20.0 1.0
C41 A:CM82001 1.3 20.0 1.0
F44 A:CM82001 2.2 20.0 1.0
F42 A:CM82001 2.2 20.0 1.0
C39 A:CM82001 2.4 20.0 1.0
C40 A:CM82001 2.7 20.0 1.0
O A:GLN204 3.3 19.9 1.0
CA A:GLN204 3.6 19.3 1.0
C38 A:CM82001 3.7 20.0 1.0
CB A:GLN204 3.8 18.8 1.0
C A:GLN204 3.8 20.1 1.0
CG A:GLN204 3.9 18.5 1.0
C35 A:CM82001 4.1 20.0 1.0
O A:HOH2366 4.3 32.5 1.0
O A:HOH2164 4.5 33.9 1.0
O A:LYS203 4.7 18.4 1.0
N A:GLN204 4.8 18.0 1.0
C37 A:CM82001 4.8 20.0 1.0
CD A:GLN204 4.9 18.1 1.0

Fluorine binding site 6 out of 6 in 2vnm

Go back to Fluorine Binding Sites List in 2vnm
Fluorine binding site 6 out of 6 in the Human Bace-1 in Complex with 3-(1,1-Dioxidotetrahydro-2H-1,2-Thiazin- 2-Yl)-5-(Ethylamino)-N-((1S,2R)-2-Hydroxy-1-(Phenylmethyl)-3-(((3- (Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human Bace-1 in Complex with 3-(1,1-Dioxidotetrahydro-2H-1,2-Thiazin- 2-Yl)-5-(Ethylamino)-N-((1S,2R)-2-Hydroxy-1-(Phenylmethyl)-3-(((3- (Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:20.0
occ:1.00
 F42 A:CM82001 0.0 20.0 1.0
C41 A:CM82001 1.3 20.0 1.0
F44 A:CM82001 2.1 20.0 1.0
F43 A:CM82001 2.2 20.0 1.0
C39 A:CM82001 2.3 20.0 1.0
C38 A:CM82001 3.0 20.0 1.0
C40 A:CM82001 3.3 20.0 1.0
C37 A:CM82001 4.3 20.0 1.0
C35 A:CM82001 4.6 20.0 1.0
C36 A:CM82001 4.9 20.0 1.0

Reference:

N.Charrier, B.Clarke, L.Cutler, E.Demont, C.Dingwall, R.Dunsdon, P.East, J.Hawkins, C.Howes, I.Hussain, P.Jeffrey, G.Maile, R.Matico, J.Mosley, A.Naylor, A.O'brien, S.Redshaw, P.Rowland, V.Soleil, K.J.Smith, S.Sweitzer, P.Theobald, D.Vesey, D.S.Walter, G.Wayne. Second Generation of Hydroxyethylamine Bace-1 Inhibitors: Optimizing Potency and Oral Bioavailability. J.Med.Chem. V. 51 3313 2008.
ISSN: ISSN 0022-2623
PubMed: 18457381
DOI: 10.1021/JM800138H
Page generated: Wed Jul 31 16:16:16 2024

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