Atomistry » Fluorine » PDB 1q6n-1rrx » 1qb1
Atomistry »
  Fluorine »
    PDB 1q6n-1rrx »
      1qb1 »

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: Wed Jul 31 12:32:11 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy