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Chlorine in PDB 5nn0: Crystal Structure of Hubche with N-((1-(2,3-Dihydro-1H-Inden-2-Yl) Piperidin-3-Yl)Methyl)-N-(2-(Dimethylamino)Ethyl)-2-Naphthamide.

Enzymatic activity of Crystal Structure of Hubche with N-((1-(2,3-Dihydro-1H-Inden-2-Yl) Piperidin-3-Yl)Methyl)-N-(2-(Dimethylamino)Ethyl)-2-Naphthamide.

All present enzymatic activity of Crystal Structure of Hubche with N-((1-(2,3-Dihydro-1H-Inden-2-Yl) Piperidin-3-Yl)Methyl)-N-(2-(Dimethylamino)Ethyl)-2-Naphthamide.:
3.1.1.8;

Protein crystallography data

The structure of Crystal Structure of Hubche with N-((1-(2,3-Dihydro-1H-Inden-2-Yl) Piperidin-3-Yl)Methyl)-N-(2-(Dimethylamino)Ethyl)-2-Naphthamide., PDB code: 5nn0 was solved by N.Coquelle, B.Brus, J.P.Colletier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.83 / 2.10
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 154.970, 154.970, 126.680, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 20.6

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Hubche with N-((1-(2,3-Dihydro-1H-Inden-2-Yl) Piperidin-3-Yl)Methyl)-N-(2-(Dimethylamino)Ethyl)-2-Naphthamide. (pdb code 5nn0). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Hubche with N-((1-(2,3-Dihydro-1H-Inden-2-Yl) Piperidin-3-Yl)Methyl)-N-(2-(Dimethylamino)Ethyl)-2-Naphthamide., PDB code: 5nn0:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 5nn0

Go back to Chlorine Binding Sites List in 5nn0
Chlorine binding site 1 out of 3 in the Crystal Structure of Hubche with N-((1-(2,3-Dihydro-1H-Inden-2-Yl) Piperidin-3-Yl)Methyl)-N-(2-(Dimethylamino)Ethyl)-2-Naphthamide.


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 Hubche with N-((1-(2,3-Dihydro-1H-Inden-2-Yl) Piperidin-3-Yl)Methyl)-N-(2-(Dimethylamino)Ethyl)-2-Naphthamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl621

b:70.2
occ:1.00
O A:HOH951 3.0 50.1 1.0
OG1 A:THR512 3.3 38.4 1.0
O A:HOH995 3.6 39.5 1.0
O A:HOH941 3.9 45.3 1.0
CB A:THR512 4.0 33.8 1.0
CG2 A:THR512 4.5 29.5 1.0
CE A:LYS513 4.6 55.0 1.0
CD A:LYS513 4.6 41.6 1.0
NZ A:LYS513 4.9 64.3 1.0

Chlorine binding site 2 out of 3 in 5nn0

Go back to Chlorine Binding Sites List in 5nn0
Chlorine binding site 2 out of 3 in the Crystal Structure of Hubche with N-((1-(2,3-Dihydro-1H-Inden-2-Yl) Piperidin-3-Yl)Methyl)-N-(2-(Dimethylamino)Ethyl)-2-Naphthamide.


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 Hubche with N-((1-(2,3-Dihydro-1H-Inden-2-Yl) Piperidin-3-Yl)Methyl)-N-(2-(Dimethylamino)Ethyl)-2-Naphthamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl622

b:79.2
occ:1.00
NH1 A:ARG265 3.3 57.1 1.0
O A:HOH986 3.4 66.9 1.0
NE A:ARG265 3.5 58.4 1.0
CZ A:ARG265 3.9 64.1 1.0
CA A:ARG40 4.3 52.0 1.0
CB A:ARG40 4.4 53.2 1.0
N A:ARG40 4.5 49.8 1.0
CG A:LYS262 4.6 62.0 1.0
CD A:ARG265 4.7 46.7 1.0
CB A:ARG265 4.8 43.6 1.0
C A:GLY39 4.9 47.0 1.0
O A:GLY39 4.9 48.8 1.0

Chlorine binding site 3 out of 3 in 5nn0

Go back to Chlorine Binding Sites List in 5nn0
Chlorine binding site 3 out of 3 in the Crystal Structure of Hubche with N-((1-(2,3-Dihydro-1H-Inden-2-Yl) Piperidin-3-Yl)Methyl)-N-(2-(Dimethylamino)Ethyl)-2-Naphthamide.


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 Hubche with N-((1-(2,3-Dihydro-1H-Inden-2-Yl) Piperidin-3-Yl)Methyl)-N-(2-(Dimethylamino)Ethyl)-2-Naphthamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl623

b:85.2
occ:1.00
NE A:ARG347 3.6 57.3 1.0
NE2 A:GLN351 3.9 52.5 1.0
NH1 A:ARG347 3.9 64.8 1.0
OE1 A:GLN351 4.2 57.4 1.0
CZ A:ARG347 4.3 62.9 1.0
CD A:GLN351 4.4 55.1 1.0
CD A:ARG347 4.7 56.4 1.0

Reference:

U.Kosak, B.Brus, D.Knez, S.Zakelj, J.Trontelj, A.Pislar, R.Sink, M.Jukic, M.Zivin, A.Podkowa, F.Nachon, X.Brazzolotto, J.Stojan, J.Kos, N.Coquelle, K.Salat, J.P.Colletier, S.Gobec. The Magic of Crystal Structure-Based Inhibitor Optimization: Development of A Butyrylcholinesterase Inhibitor with Picomolar Affinity and in Vivo Activity. J. Med. Chem. V. 61 119 2018.
ISSN: ISSN 1520-4804
PubMed: 29227101
DOI: 10.1021/ACS.JMEDCHEM.7B01086
Page generated: Sat Dec 12 12:10:07 2020

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