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Fluorine in PDB 1qb1: Bovine Trypsin with 1-[2-[5-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1-Methyl-1H-Imidazol-2-Yl)Phenoxy]Pyridin-4- Yl]Piperidine-3-Carboxylic Acid (Zk-806974)

Enzymatic activity of Bovine Trypsin with 1-[2-[5-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1-Methyl-1H-Imidazol-2-Yl)Phenoxy]Pyridin-4- Yl]Piperidine-3-Carboxylic Acid (Zk-806974)

All present enzymatic activity of Bovine Trypsin with 1-[2-[5-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1-Methyl-1H-Imidazol-2-Yl)Phenoxy]Pyridin-4- Yl]Piperidine-3-Carboxylic Acid (Zk-806974):
3.4.21.4;

Protein crystallography data

The structure of Bovine Trypsin with 1-[2-[5-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1-Methyl-1H-Imidazol-2-Yl)Phenoxy]Pyridin-4- Yl]Piperidine-3-Carboxylic Acid (Zk-806974), PDB code: 1qb1 was solved by M.Whitlow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.160, 63.780, 69.350, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 23.7

Other elements in 1qb1:

The structure of Bovine Trypsin with 1-[2-[5-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1-Methyl-1H-Imidazol-2-Yl)Phenoxy]Pyridin-4- Yl]Piperidine-3-Carboxylic Acid (Zk-806974) also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Bovine Trypsin with 1-[2-[5-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1-Methyl-1H-Imidazol-2-Yl)Phenoxy]Pyridin-4- Yl]Piperidine-3-Carboxylic Acid (Zk-806974) (pdb code 1qb1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Bovine Trypsin with 1-[2-[5-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1-Methyl-1H-Imidazol-2-Yl)Phenoxy]Pyridin-4- Yl]Piperidine-3-Carboxylic Acid (Zk-806974), PDB code: 1qb1:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 1qb1

Go back to Fluorine Binding Sites List in 1qb1
Fluorine binding site 1 out of 2 in the Bovine Trypsin with 1-[2-[5-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1-Methyl-1H-Imidazol-2-Yl)Phenoxy]Pyridin-4- Yl]Piperidine-3-Carboxylic Acid (Zk-806974)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Bovine Trypsin with 1-[2-[5-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1-Methyl-1H-Imidazol-2-Yl)Phenoxy]Pyridin-4- Yl]Piperidine-3-Carboxylic Acid (Zk-806974) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F300

b:46.3
occ:1.00
 F1 A:974300 0.0 46.3 1.0
C1 A:974300 1.3 45.8 1.0
C6 A:974300 2.3 41.1 1.0
C2 A:974300 2.4 48.8 1.0
CG A:GLN180 2.6 34.2 1.0
C32 A:974300 2.7 54.1 1.0
N31 A:974300 2.8 51.9 0.5
O1 A:974300 2.8 29.8 1.0
CD A:GLN180 2.9 38.8 1.0
NE2 A:GLN180 3.3 43.0 1.0
OE1 A:GLN180 3.5 41.4 1.0
N5 A:974300 3.6 42.2 1.0
C3 A:974300 3.6 48.2 1.0
C36 A:974300 4.0 53.2 1.0
C4 A:974300 4.1 46.9 1.0
C11 A:974300 4.1 33.0 1.0
CB A:GLN180 4.1 25.6 1.0
C33 A:974300 4.2 55.7 1.0
F2 A:974300 4.7 48.5 1.0
O11 A:974300 4.7 26.4 1.0
CA A:GLN180 4.9 18.2 1.0
C16 A:974300 4.9 24.3 1.0
C37 A:974300 4.9 56.4 1.0
N A:GLN180 5.0 15.1 1.0

Fluorine binding site 2 out of 2 in 1qb1

Go back to Fluorine Binding Sites List in 1qb1
Fluorine binding site 2 out of 2 in the Bovine Trypsin with 1-[2-[5-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1-Methyl-1H-Imidazol-2-Yl)Phenoxy]Pyridin-4- Yl]Piperidine-3-Carboxylic Acid (Zk-806974)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Bovine Trypsin with 1-[2-[5-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1-Methyl-1H-Imidazol-2-Yl)Phenoxy]Pyridin-4- Yl]Piperidine-3-Carboxylic Acid (Zk-806974) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F300

b:48.5
occ:1.00
 F2 A:974300 0.0 48.5 1.0
C3 A:974300 1.3 48.2 1.0
C2 A:974300 2.3 48.8 1.0
C4 A:974300 2.4 46.9 1.0
N31 A:974300 2.7 51.9 0.5
C36 A:974300 2.8 53.2 1.0
O2 A:974300 2.8 48.1 1.0
C21 A:974300 3.2 49.2 1.0
C22 A:974300 3.5 50.1 1.0
C35 A:974300 3.6 54.8 1.0
N5 A:974300 3.6 42.2 1.0
C1 A:974300 3.6 45.8 1.0
C26 A:974300 3.9 49.7 1.0
C32 A:974300 4.1 54.1 1.0
C6 A:974300 4.1 41.1 1.0
C23 A:974300 4.5 51.1 1.0
C33 A:974300 4.5 55.7 1.0
F1 A:974300 4.7 46.3 1.0
C34 A:974300 4.7 55.4 1.0
C25 A:974300 4.8 51.1 1.0

Reference:

M.Whitlow, D.O.Arnaiz, B.O.Buckman, D.D.Davey, B.Griedel, W.J.Guilford, S.K.Koovakkat, A.Liang, R.Mohan, G.B.Phillips, M.Seto, K.J.Shaw, W.Xu, Z.Zhao, D.R.Light, M.M.Morrissey. Crystallographic Analysis of Potent and Selective Factor Xa Inhibitors Complexed to Bovine Trypsin. Acta Crystallogr.,Sect.D V. 55 1395 1999.
ISSN: ISSN 0907-4449
PubMed: 10417407
DOI: 10.1107/S0907444999007350
Page generated: Sun Dec 13 11:32:12 2020

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