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Fluorine in PDB 2vnn: Human Bace-1 in Complex with 7-Ethyl-N-((1S,2R)-2-Hydroxy-1- (Phenylmethyl)-3-(((3-(Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)-1- Methyl-3,4-Dihydro-1H-(1,2,5)Thiadiazepino(3,4,5-Hi)Indole-9- Carboxamide 2,2-Dioxide

Enzymatic activity of Human Bace-1 in Complex with 7-Ethyl-N-((1S,2R)-2-Hydroxy-1- (Phenylmethyl)-3-(((3-(Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)-1- Methyl-3,4-Dihydro-1H-(1,2,5)Thiadiazepino(3,4,5-Hi)Indole-9- Carboxamide 2,2-Dioxide

All present enzymatic activity of Human Bace-1 in Complex with 7-Ethyl-N-((1S,2R)-2-Hydroxy-1- (Phenylmethyl)-3-(((3-(Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)-1- Methyl-3,4-Dihydro-1H-(1,2,5)Thiadiazepino(3,4,5-Hi)Indole-9- Carboxamide 2,2-Dioxide:
3.4.23.46;

Protein crystallography data

The structure of Human Bace-1 in Complex with 7-Ethyl-N-((1S,2R)-2-Hydroxy-1- (Phenylmethyl)-3-(((3-(Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)-1- Methyl-3,4-Dihydro-1H-(1,2,5)Thiadiazepino(3,4,5-Hi)Indole-9- Carboxamide 2,2-Dioxide, PDB code: 2vnn 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) 61.78 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.469, 76.699, 104.174, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 21.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Bace-1 in Complex with 7-Ethyl-N-((1S,2R)-2-Hydroxy-1- (Phenylmethyl)-3-(((3-(Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)-1- Methyl-3,4-Dihydro-1H-(1,2,5)Thiadiazepino(3,4,5-Hi)Indole-9- Carboxamide 2,2-Dioxide (pdb code 2vnn). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Human Bace-1 in Complex with 7-Ethyl-N-((1S,2R)-2-Hydroxy-1- (Phenylmethyl)-3-(((3-(Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)-1- Methyl-3,4-Dihydro-1H-(1,2,5)Thiadiazepino(3,4,5-Hi)Indole-9- Carboxamide 2,2-Dioxide, PDB code: 2vnn:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 2vnn

Go back to Fluorine Binding Sites List in 2vnn
Fluorine binding site 1 out of 3 in the Human Bace-1 in Complex with 7-Ethyl-N-((1S,2R)-2-Hydroxy-1- (Phenylmethyl)-3-(((3-(Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)-1- Methyl-3,4-Dihydro-1H-(1,2,5)Thiadiazepino(3,4,5-Hi)Indole-9- Carboxamide 2,2-Dioxide


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 7-Ethyl-N-((1S,2R)-2-Hydroxy-1- (Phenylmethyl)-3-(((3-(Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)-1- Methyl-3,4-Dihydro-1H-(1,2,5)Thiadiazepino(3,4,5-Hi)Indole-9- Carboxamide 2,2-Dioxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2000

b:26.7
occ:1.00
 F42 A:CM72000 0.0 26.7 1.0
C41 A:CM72000 1.3 23.8 1.0
F43 A:CM72000 2.2 27.3 1.0
F44 A:CM72000 2.2 28.0 1.0
C39 A:CM72000 2.4 22.6 1.0
C40 A:CM72000 2.9 21.2 1.0
O A:HOH2034 3.5 12.0 1.0
C38 A:CM72000 3.6 21.3 1.0
O A:HOH2162 3.7 28.8 1.0
CD1 A:ILE187 3.7 13.8 1.0
O A:ILE187 3.9 12.8 1.0
CB A:SER96 4.0 9.7 1.0
OH A:TYR259 4.0 18.0 1.0
O A:GLY95 4.1 11.1 1.0
CA A:SER96 4.1 9.8 1.0
CB A:ILE187 4.2 14.1 1.0
CE1 A:TYR259 4.2 15.0 1.0
C35 A:CM72000 4.3 20.5 1.0
CG1 A:ILE187 4.3 11.8 1.0
CZ A:TYR259 4.4 17.0 1.0
C37 A:CM72000 4.8 21.4 1.0
C A:ILE187 4.8 13.4 1.0
N A:SER97 4.9 10.0 1.0
CG2 A:ILE187 5.0 14.7 1.0
C A:GLY95 5.0 10.6 1.0

Fluorine binding site 2 out of 3 in 2vnn

Go back to Fluorine Binding Sites List in 2vnn
Fluorine binding site 2 out of 3 in the Human Bace-1 in Complex with 7-Ethyl-N-((1S,2R)-2-Hydroxy-1- (Phenylmethyl)-3-(((3-(Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)-1- Methyl-3,4-Dihydro-1H-(1,2,5)Thiadiazepino(3,4,5-Hi)Indole-9- Carboxamide 2,2-Dioxide


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 7-Ethyl-N-((1S,2R)-2-Hydroxy-1- (Phenylmethyl)-3-(((3-(Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)-1- Methyl-3,4-Dihydro-1H-(1,2,5)Thiadiazepino(3,4,5-Hi)Indole-9- Carboxamide 2,2-Dioxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2000

b:27.3
occ:1.00
 F43 A:CM72000 0.0 27.3 1.0
C41 A:CM72000 1.3 23.8 1.0
F42 A:CM72000 2.2 26.7 1.0
F44 A:CM72000 2.2 28.0 1.0
C39 A:CM72000 2.3 22.6 1.0
C40 A:CM72000 3.0 21.2 1.0
CB A:SER96 3.2 9.7 1.0
C38 A:CM72000 3.4 21.3 1.0
CE1 A:TYR132 3.4 14.6 1.0
CD1 A:TYR132 3.5 15.8 1.0
O A:HOH2034 3.5 12.0 1.0
CG1 A:VAL130 3.8 17.5 1.0
CA A:SER96 4.1 9.8 1.0
OG A:SER96 4.3 9.9 1.0
C35 A:CM72000 4.4 20.5 1.0
O A:GLY95 4.4 11.1 1.0
O31 A:CM72000 4.5 14.1 1.0
CZ A:TYR132 4.6 16.0 1.0
C37 A:CM72000 4.6 21.4 1.0
CG A:TYR132 4.7 17.0 1.0
O A:HOH2033 4.8 16.0 1.0
N A:SER97 4.9 10.0 1.0

Fluorine binding site 3 out of 3 in 2vnn

Go back to Fluorine Binding Sites List in 2vnn
Fluorine binding site 3 out of 3 in the Human Bace-1 in Complex with 7-Ethyl-N-((1S,2R)-2-Hydroxy-1- (Phenylmethyl)-3-(((3-(Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)-1- Methyl-3,4-Dihydro-1H-(1,2,5)Thiadiazepino(3,4,5-Hi)Indole-9- Carboxamide 2,2-Dioxide


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 7-Ethyl-N-((1S,2R)-2-Hydroxy-1- (Phenylmethyl)-3-(((3-(Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)-1- Methyl-3,4-Dihydro-1H-(1,2,5)Thiadiazepino(3,4,5-Hi)Indole-9- Carboxamide 2,2-Dioxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2000

b:28.0
occ:1.00
 F44 A:CM72000 0.0 28.0 1.0
C41 A:CM72000 1.3 23.8 1.0
F42 A:CM72000 2.2 26.7 1.0
F43 A:CM72000 2.2 27.3 1.0
C39 A:CM72000 2.4 22.6 1.0
C38 A:CM72000 2.8 21.3 1.0
O A:HOH2162 3.4 28.8 1.0
C40 A:CM72000 3.7 21.2 1.0
NE A:ARG189 3.9 32.6 1.0
NH2 A:ARG189 3.9 35.8 1.0
CG1 A:VAL130 4.1 17.5 1.0
O A:HOH2034 4.2 12.0 1.0
C37 A:CM72000 4.2 21.4 1.0
O A:PRO131 4.2 17.2 1.0
CZ A:ARG189 4.3 34.5 1.0
O A:ILE187 4.5 12.8 1.0
CG A:ARG189 4.6 21.2 1.0
C35 A:CM72000 4.9 20.5 1.0
CD A:ARG189 4.9 26.7 1.0
CD A:PRO131 5.0 18.7 1.0
CD1 A:TYR132 5.0 15.8 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: Mon Jul 14 14:32:21 2025

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