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Fluorine in PDB 3q8w: A B-Aminoacyl Containing Thiazolidine Derivative and Dppiv Complex

Enzymatic activity of A B-Aminoacyl Containing Thiazolidine Derivative and Dppiv Complex

All present enzymatic activity of A B-Aminoacyl Containing Thiazolidine Derivative and Dppiv Complex:
3.4.14.5;

Protein crystallography data

The structure of A B-Aminoacyl Containing Thiazolidine Derivative and Dppiv Complex, PDB code: 3q8w was solved by J.O.Lee, D.H.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.47 / 3.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 118.412, 124.501, 133.119, 90.00, 90.00, 90.00
R / Rfree (%) 28.2 / 32.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the A B-Aminoacyl Containing Thiazolidine Derivative and Dppiv Complex (pdb code 3q8w). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the A B-Aminoacyl Containing Thiazolidine Derivative and Dppiv Complex, PDB code: 3q8w:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3q8w

Go back to Fluorine Binding Sites List in 3q8w
Fluorine binding site 1 out of 6 in the A B-Aminoacyl Containing Thiazolidine Derivative and Dppiv Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of A B-Aminoacyl Containing Thiazolidine Derivative and Dppiv Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:53.6
occ:1.00
 FAL A:AZV1 0.0 53.6 1.0
CAK A:AZV1 1.3 54.0 1.0
CAJ A:AZV1 2.4 56.2 1.0
CAM A:AZV1 2.4 53.0 1.0
FAN A:AZV1 2.8 47.8 1.0
CD2 A:TYR631 3.4 52.5 1.0
CE1 A:TYR666 3.6 55.3 1.0
CAO A:AZV1 3.6 54.0 1.0
CAI A:AZV1 3.6 57.4 1.0
CZ A:TYR666 3.7 54.9 1.0
OH A:TYR666 3.7 55.3 1.0
CB A:TYR631 4.0 52.1 1.0
CG A:TYR631 4.0 51.7 1.0
CAP A:AZV1 4.1 55.8 1.0
CE2 A:TYR631 4.2 51.2 1.0
CE2 A:TYR662 4.3 51.2 1.0
CD1 A:TYR666 4.3 54.7 1.0
CH2 A:TRP659 4.4 48.5 1.0
CA A:TYR631 4.4 52.7 1.0
CZ A:TYR662 4.5 49.8 1.0
CE2 A:TYR666 4.5 54.3 1.0
CG2 A:VAL656 4.5 48.2 1.0
OH A:TYR662 4.6 48.8 1.0
CZ3 A:TRP659 4.6 49.3 1.0
N A:TYR631 4.7 53.3 1.0
CD2 A:TYR662 4.8 52.7 1.0
CAH A:AZV1 4.9 61.1 1.0
OH A:TYR547 4.9 61.4 1.0

Fluorine binding site 2 out of 6 in 3q8w

Go back to Fluorine Binding Sites List in 3q8w
Fluorine binding site 2 out of 6 in the A B-Aminoacyl Containing Thiazolidine Derivative and Dppiv Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of A B-Aminoacyl Containing Thiazolidine Derivative and Dppiv Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:47.8
occ:1.00
 FAN A:AZV1 0.0 47.8 1.0
CAM A:AZV1 1.3 53.0 1.0
CAO A:AZV1 2.4 54.0 1.0
CAK A:AZV1 2.4 54.0 1.0
FAL A:AZV1 2.8 53.6 1.0
CG2 A:VAL656 3.4 48.2 1.0
CG2 A:VAL711 3.4 44.2 1.0
CAP A:AZV1 3.6 55.8 1.0
CAJ A:AZV1 3.6 56.2 1.0
N A:TYR631 4.0 53.3 1.0
CAI A:AZV1 4.2 57.4 1.0
CE1 A:TYR662 4.2 49.4 1.0
C A:SER630 4.2 53.7 1.0
CZ A:TYR662 4.2 49.8 1.0
CA A:TYR631 4.4 52.7 1.0
OH A:TYR662 4.5 48.8 1.0
CB A:SER630 4.5 55.5 1.0
CD1 A:TYR662 4.6 50.7 1.0
O A:SER630 4.6 52.6 1.0
CA A:SER630 4.7 54.7 1.0
CB A:VAL656 4.7 47.2 1.0
CE2 A:TYR662 4.7 51.2 1.0
FAQ A:AZV1 4.7 57.4 1.0
CB A:TYR631 4.8 52.1 1.0
CB A:VAL711 4.8 44.1 1.0
CG1 A:VAL656 5.0 45.8 1.0

Fluorine binding site 3 out of 6 in 3q8w

Go back to Fluorine Binding Sites List in 3q8w
Fluorine binding site 3 out of 6 in the A B-Aminoacyl Containing Thiazolidine Derivative and Dppiv Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of A B-Aminoacyl Containing Thiazolidine Derivative and Dppiv Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:57.4
occ:1.00
 FAQ A:AZV1 0.0 57.4 1.0
CAP A:AZV1 1.3 55.8 1.0
CAO A:AZV1 2.4 54.0 1.0
CAI A:AZV1 2.4 57.4 1.0
CAH A:AZV1 2.9 61.1 1.0
NH2 A:ARG125 3.0 56.9 1.0
OE2 A:GLU205 3.3 50.2 1.0
OXT A:AZV1 3.4 63.5 1.0
CAJ A:AZV1 3.6 56.2 1.0
CAM A:AZV1 3.6 53.0 1.0
CD2 A:HIS740 3.6 52.1 1.0
ND2 A:ASN710 3.7 48.2 1.0
NE2 A:HIS740 3.7 51.2 1.0
CG A:ASN710 3.8 47.5 1.0
NAG A:AZV1 3.9 64.4 1.0
OD1 A:ASN710 3.9 48.3 1.0
CZ A:ARG125 4.0 56.4 1.0
CAF A:AZV1 4.0 64.2 1.0
CAK A:AZV1 4.1 54.0 1.0
OH A:TYR662 4.2 48.8 1.0
C A:AZV1 4.4 65.1 1.0
NH1 A:ARG125 4.5 56.5 1.0
CG A:HIS740 4.5 51.9 1.0
CD A:GLU205 4.5 50.6 1.0
CE1 A:HIS740 4.6 51.0 1.0
CB A:SER630 4.7 55.5 1.0
FAN A:AZV1 4.7 47.8 1.0
CB A:ASN710 4.7 46.6 1.0
O A:AZV1 4.7 63.6 1.0
NE A:ARG125 4.9 56.1 1.0
CAE A:AZV1 4.9 65.9 1.0

Fluorine binding site 4 out of 6 in 3q8w

Go back to Fluorine Binding Sites List in 3q8w
Fluorine binding site 4 out of 6 in the A B-Aminoacyl Containing Thiazolidine Derivative and Dppiv Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of A B-Aminoacyl Containing Thiazolidine Derivative and Dppiv Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:60.3
occ:1.00
 FAL B:AZV1 0.0 60.3 1.0
CAK B:AZV1 1.3 59.2 1.0
CAJ B:AZV1 2.3 58.1 1.0
CAM B:AZV1 2.4 58.0 1.0
FAN B:AZV1 2.8 57.8 1.0
NE2 B:HIS740 3.0 51.6 1.0
CG2 B:VAL711 3.2 43.1 1.0
CE1 B:HIS740 3.2 51.7 1.0
CD2 B:HIS740 3.6 51.7 1.0
CAO B:AZV1 3.6 57.5 1.0
OD1 B:ASN710 3.6 45.0 1.0
CAI B:AZV1 3.6 58.5 1.0
CG B:ASN710 3.8 45.7 1.0
ND1 B:HIS740 3.8 52.6 1.0
CB B:SER630 3.9 56.4 1.0
OH B:TYR662 4.0 50.5 1.0
CG B:HIS740 4.0 52.0 1.0
CAP B:AZV1 4.1 58.5 1.0
CB B:ASN710 4.1 45.0 1.0
CE1 B:TYR662 4.3 53.4 1.0
ND2 B:ASN710 4.4 47.1 1.0
CZ B:TYR662 4.4 52.7 1.0
N B:VAL711 4.5 42.7 1.0
CB B:VAL711 4.5 42.6 1.0
CA B:SER630 4.6 55.3 1.0
OXT B:AZV1 4.8 69.7 1.0
OG B:SER630 4.8 58.0 1.0
CAH B:AZV1 4.8 58.1 1.0

Fluorine binding site 5 out of 6 in 3q8w

Go back to Fluorine Binding Sites List in 3q8w
Fluorine binding site 5 out of 6 in the A B-Aminoacyl Containing Thiazolidine Derivative and Dppiv Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of A B-Aminoacyl Containing Thiazolidine Derivative and Dppiv Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:57.8
occ:1.00
 FAN B:AZV1 0.0 57.8 1.0
CAM B:AZV1 1.3 58.0 1.0
CAO B:AZV1 2.4 57.5 1.0
CAK B:AZV1 2.4 59.2 1.0
FAL B:AZV1 2.8 60.3 1.0
CG2 B:VAL656 3.4 46.8 1.0
N B:TYR631 3.5 52.1 1.0
CG2 B:VAL711 3.6 43.1 1.0
CAP B:AZV1 3.6 58.5 1.0
CAJ B:AZV1 3.7 58.1 1.0
C B:SER630 3.7 53.5 1.0
CA B:TYR631 3.9 51.6 1.0
CB B:SER630 4.0 56.4 1.0
O B:SER630 4.1 52.8 1.0
CA B:SER630 4.2 55.3 1.0
CAI B:AZV1 4.2 58.5 1.0
CB B:TYR631 4.3 52.4 1.0
OG B:SER630 4.6 58.0 1.0
CE1 B:TYR662 4.7 53.4 1.0
CZ B:TYR662 4.7 52.7 1.0
FAQ B:AZV1 4.7 58.2 1.0
CB B:VAL656 4.8 46.1 1.0
OH B:TYR662 4.8 50.5 1.0
CE1 B:HIS740 4.9 51.7 1.0
NE2 B:HIS740 4.9 51.6 1.0
O B:ALA654 4.9 49.3 1.0
N B:VAL656 5.0 46.7 1.0

Fluorine binding site 6 out of 6 in 3q8w

Go back to Fluorine Binding Sites List in 3q8w
Fluorine binding site 6 out of 6 in the A B-Aminoacyl Containing Thiazolidine Derivative and Dppiv Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of A B-Aminoacyl Containing Thiazolidine Derivative and Dppiv Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:58.2
occ:1.00
 FAQ B:AZV1 0.0 58.2 1.0
CAP B:AZV1 1.3 58.5 1.0
CAO B:AZV1 2.3 57.5 1.0
CAI B:AZV1 2.4 58.5 1.0
CAH B:AZV1 2.9 58.1 1.0
OH B:TYR666 3.1 55.4 1.0
OH B:TYR547 3.1 60.5 1.0
CAF B:AZV1 3.2 58.4 1.0
CZ B:TYR666 3.3 54.2 1.0
CE2 B:TYR666 3.5 54.0 1.0
CAJ B:AZV1 3.6 58.1 1.0
CAM B:AZV1 3.6 58.0 1.0
NAG B:AZV1 4.0 55.9 1.0
CAK B:AZV1 4.1 59.2 1.0
CE1 B:TYR666 4.1 53.1 1.0
OAD B:AZV1 4.1 57.5 1.0
CD2 B:TYR631 4.2 52.8 1.0
CD2 B:TYR666 4.3 53.0 1.0
CZ B:TYR547 4.4 61.9 1.0
CAE B:AZV1 4.4 58.9 1.0
CAC B:AZV1 4.7 59.8 1.0
CB B:TYR631 4.7 52.4 1.0
FAN B:AZV1 4.7 57.8 1.0
CD1 B:TYR666 4.9 52.4 1.0
OH B:TYR662 5.0 50.5 1.0
CG B:TYR631 5.0 53.2 1.0

Reference:

W.S.Park, S.K.Kang, M.A.Jun, M.S.Shin, K.Y.Kim, S.D.Rhee, M.A.Bae, M.S.Kim, K.R.Kim, N.S.Kang, S.E.Yoo, J.O.Lee, D.H.Song, P.Silinski, S.E.Schneider, J.H.Ahn, S.S.Kim. Discovery of B-Aminoacyl Containing Thiazolidine Derivatives As Potent and Selective Dipeptidyl Peptidase IV Inhibitors To Be Published.
Page generated: Wed Jul 31 21:57:52 2024

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