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Fluorine in PDB 3hac: The Structure of Dpp-4 in Complex with Piperidine Fused Imidazopyridine 34

Enzymatic activity of The Structure of Dpp-4 in Complex with Piperidine Fused Imidazopyridine 34

All present enzymatic activity of The Structure of Dpp-4 in Complex with Piperidine Fused Imidazopyridine 34:
3.4.14.5;

Protein crystallography data

The structure of The Structure of Dpp-4 in Complex with Piperidine Fused Imidazopyridine 34, PDB code: 3hac was solved by G.Scapin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 118.120, 125.496, 136.902, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 20.5

Other elements in 3hac:

The structure of The Structure of Dpp-4 in Complex with Piperidine Fused Imidazopyridine 34 also contains other interesting chemical elements:

Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The Structure of Dpp-4 in Complex with Piperidine Fused Imidazopyridine 34 (pdb code 3hac). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the The Structure of Dpp-4 in Complex with Piperidine Fused Imidazopyridine 34, PDB code: 3hac:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3hac

Go back to Fluorine Binding Sites List in 3hac
Fluorine binding site 1 out of 6 in the The Structure of Dpp-4 in Complex with Piperidine Fused Imidazopyridine 34


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Structure of Dpp-4 in Complex with Piperidine Fused Imidazopyridine 34 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F767

b:35.5
occ:1.00
 F21 A:361767 0.0 35.5 1.0
C5 A:361767 1.3 34.8 1.0
C6 A:361767 2.4 34.4 1.0
C4 A:361767 2.4 31.8 1.0
F27 A:361767 2.7 35.9 1.0
CD2 A:TYR631 3.4 32.6 1.0
CE1 A:TYR666 3.4 32.7 1.0
CZ A:TYR666 3.6 33.2 1.0
OH A:TYR666 3.6 32.1 1.0
C1 A:361767 3.6 34.7 1.0
C3 A:361767 3.6 34.4 1.0
CB A:TYR631 3.8 31.9 1.0
CH2 A:TRP659 3.9 31.1 1.0
CG A:TYR631 4.0 33.0 1.0
C2 A:361767 4.1 34.1 1.0
CD1 A:TYR666 4.2 32.2 1.0
CA A:TYR631 4.2 31.9 1.0
CE2 A:TYR662 4.2 30.0 1.0
CZ3 A:TRP659 4.2 29.8 1.0
N A:TYR631 4.3 32.0 1.0
CG2 A:VAL656 4.4 28.8 1.0
CE2 A:TYR631 4.4 32.2 1.0
CE2 A:TYR666 4.4 33.0 1.0
O A:HOH1044 4.4 34.5 1.0
CZ A:TYR662 4.5 29.7 1.0
CD2 A:TYR662 4.6 28.8 1.0
OH A:TYR547 4.7 39.5 1.0
OH A:TYR662 4.7 31.5 1.0
OG A:SER630 4.8 37.5 1.0
C9 A:361767 4.9 33.6 1.0
CG A:TYR666 4.9 32.2 1.0
CD2 A:TYR666 5.0 32.3 1.0

Fluorine binding site 2 out of 6 in 3hac

Go back to Fluorine Binding Sites List in 3hac
Fluorine binding site 2 out of 6 in the The Structure of Dpp-4 in Complex with Piperidine Fused Imidazopyridine 34


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Structure of Dpp-4 in Complex with Piperidine Fused Imidazopyridine 34 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F767

b:35.9
occ:1.00
 F27 A:361767 0.0 35.9 1.0
C6 A:361767 1.3 34.4 1.0
C5 A:361767 2.4 34.8 1.0
C1 A:361767 2.4 34.7 1.0
F21 A:361767 2.7 35.5 1.0
CG2 A:VAL656 3.2 28.8 1.0
CG2 A:VAL711 3.2 31.5 1.0
OG A:SER630 3.3 37.5 1.0
C2 A:361767 3.6 34.1 1.0
C4 A:361767 3.6 31.8 1.0
N A:TYR631 3.7 32.0 1.0
C A:SER630 4.0 32.4 1.0
CZ A:TYR662 4.1 29.7 1.0
CE1 A:TYR662 4.1 30.4 1.0
C3 A:361767 4.1 34.4 1.0
CA A:SER630 4.3 32.4 1.0
OH A:TYR662 4.3 31.5 1.0
CA A:TYR631 4.4 31.9 1.0
CB A:SER630 4.4 32.4 1.0
CB A:VAL656 4.4 29.8 1.0
O A:SER630 4.5 32.0 1.0
NE2 A:HIS740 4.5 32.8 1.0
CD1 A:TYR662 4.6 30.4 1.0
CE2 A:TYR662 4.6 30.0 1.0
CB A:VAL711 4.6 31.6 1.0
F22 A:361767 4.7 35.8 1.0
CE1 A:HIS740 4.7 32.6 1.0
N A:VAL656 4.8 30.4 1.0
CB A:TYR631 4.8 31.9 1.0
CD2 A:TYR662 5.0 28.8 1.0

Fluorine binding site 3 out of 6 in 3hac

Go back to Fluorine Binding Sites List in 3hac
Fluorine binding site 3 out of 6 in the The Structure of Dpp-4 in Complex with Piperidine Fused Imidazopyridine 34


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The Structure of Dpp-4 in Complex with Piperidine Fused Imidazopyridine 34 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F767

b:35.8
occ:1.00
 F22 A:361767 0.0 35.8 1.0
C2 A:361767 1.3 34.1 1.0
C1 A:361767 2.3 34.7 1.0
C3 A:361767 2.4 34.4 1.0
C9 A:361767 2.8 33.6 1.0
NH2 A:ARG125 3.0 33.5 1.0
ND2 A:ASN710 3.2 31.4 1.0
OE2 A:GLU205 3.3 32.9 1.0
N23 A:361767 3.3 28.7 1.0
O A:HOH1338 3.4 37.4 1.0
O A:HOH801 3.6 31.4 1.0
OH A:TYR662 3.6 31.5 1.0
C6 A:361767 3.6 34.4 1.0
C4 A:361767 3.6 31.8 1.0
C14 A:361767 3.6 32.2 1.0
CG A:ASN710 3.9 32.2 1.0
CD2 A:HIS740 3.9 34.1 1.0
OD1 A:ASN710 3.9 34.5 1.0
NE2 A:HIS740 4.0 32.8 1.0
OG A:SER630 4.0 37.5 1.0
C10 A:361767 4.1 33.2 1.0
C5 A:361767 4.1 34.8 1.0
CZ A:ARG125 4.3 36.0 1.0
CD A:GLU205 4.5 33.3 1.0
C13 A:361767 4.6 33.6 1.0
O A:HOH869 4.7 46.8 1.0
F27 A:361767 4.7 35.9 1.0
CZ A:TYR662 4.8 29.7 1.0
CG A:HIS740 5.0 33.0 1.0

Fluorine binding site 4 out of 6 in 3hac

Go back to Fluorine Binding Sites List in 3hac
Fluorine binding site 4 out of 6 in the The Structure of Dpp-4 in Complex with Piperidine Fused Imidazopyridine 34


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of The Structure of Dpp-4 in Complex with Piperidine Fused Imidazopyridine 34 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:34.8
occ:1.00
 F21 B:3612 0.0 34.8 1.0
C5 B:3612 1.3 36.0 1.0
C6 B:3612 2.3 34.6 1.0
C4 B:3612 2.4 35.1 1.0
F27 B:3612 2.7 34.9 1.0
CE1 B:TYR666 3.4 32.8 1.0
CD2 B:TYR631 3.5 30.2 1.0
CZ B:TYR666 3.5 31.5 1.0
OH B:TYR666 3.5 31.9 1.0
C1 B:3612 3.6 35.1 1.0
C3 B:3612 3.6 35.2 1.0
CB B:TYR631 3.9 30.6 1.0
CH2 B:TRP659 4.0 32.0 1.0
C2 B:3612 4.1 34.6 1.0
CG B:TYR631 4.1 29.6 1.0
CD1 B:TYR666 4.2 32.2 1.0
CE2 B:TYR662 4.2 30.5 1.0
CA B:TYR631 4.3 30.5 1.0
CZ3 B:TRP659 4.3 33.5 1.0
CE2 B:TYR666 4.3 31.5 1.0
N B:TYR631 4.3 30.8 1.0
CG2 B:VAL656 4.4 29.9 1.0
O B:HOH1066 4.4 33.4 1.0
CE2 B:TYR631 4.5 30.3 1.0
CZ B:TYR662 4.5 31.6 1.0
CD2 B:TYR662 4.6 30.6 1.0
OH B:TYR547 4.7 36.8 1.0
OG B:SER630 4.7 35.5 1.0
OH B:TYR662 4.7 32.6 1.0
C9 B:3612 4.9 33.5 1.0
CG B:TYR666 4.9 31.6 1.0
CD2 B:TYR666 4.9 31.4 1.0

Fluorine binding site 5 out of 6 in 3hac

Go back to Fluorine Binding Sites List in 3hac
Fluorine binding site 5 out of 6 in the The Structure of Dpp-4 in Complex with Piperidine Fused Imidazopyridine 34


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of The Structure of Dpp-4 in Complex with Piperidine Fused Imidazopyridine 34 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:34.9
occ:1.00
 F27 B:3612 0.0 34.9 1.0
C6 B:3612 1.3 34.6 1.0
C5 B:3612 2.3 36.0 1.0
C1 B:3612 2.4 35.1 1.0
F21 B:3612 2.7 34.8 1.0
CG2 B:VAL711 3.2 28.9 1.0
CG2 B:VAL656 3.2 29.9 1.0
OG B:SER630 3.3 35.5 1.0
C4 B:3612 3.6 35.1 1.0
C2 B:3612 3.7 34.6 1.0
N B:TYR631 3.8 30.8 1.0
CZ B:TYR662 4.0 31.6 1.0
C B:SER630 4.1 32.0 1.0
CE1 B:TYR662 4.1 30.9 1.0
C3 B:3612 4.1 35.2 1.0
OH B:TYR662 4.3 32.6 1.0
CA B:SER630 4.4 32.1 1.0
CB B:SER630 4.4 32.0 1.0
CA B:TYR631 4.5 30.5 1.0
CE2 B:TYR662 4.5 30.5 1.0
CB B:VAL656 4.5 30.4 1.0
CD1 B:TYR662 4.5 29.4 1.0
NE2 B:HIS740 4.6 34.3 1.0
O B:SER630 4.6 32.1 1.0
CB B:VAL711 4.6 30.6 1.0
CE1 B:HIS740 4.7 33.4 1.0
F22 B:3612 4.8 33.6 1.0
CD2 B:TYR662 4.9 30.6 1.0
N B:VAL656 4.9 29.6 1.0
CB B:TYR631 4.9 30.6 1.0
CG B:TYR662 4.9 30.2 1.0
O B:HOH976 5.0 27.8 1.0

Fluorine binding site 6 out of 6 in 3hac

Go back to Fluorine Binding Sites List in 3hac
Fluorine binding site 6 out of 6 in the The Structure of Dpp-4 in Complex with Piperidine Fused Imidazopyridine 34


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of The Structure of Dpp-4 in Complex with Piperidine Fused Imidazopyridine 34 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:33.6
occ:1.00
 F22 B:3612 0.0 33.6 1.0
C2 B:3612 1.3 34.6 1.0
C1 B:3612 2.4 35.1 1.0
C3 B:3612 2.4 35.2 1.0
C9 B:3612 2.8 33.5 1.0
NH2 B:ARG125 2.9 35.9 1.0
ND2 B:ASN710 3.2 33.6 1.0
OE2 B:GLU205 3.3 33.8 1.0
N23 B:3612 3.3 30.6 1.0
O B:HOH945 3.4 45.8 1.0
O B:HOH976 3.6 27.8 1.0
C6 B:3612 3.6 34.6 1.0
C4 B:3612 3.6 35.1 1.0
C14 B:3612 3.7 33.8 1.0
OH B:TYR662 3.7 32.6 1.0
CG B:ASN710 3.8 33.0 1.0
OD1 B:ASN710 3.8 33.6 1.0
CD2 B:HIS740 3.8 33.5 1.0
NE2 B:HIS740 4.0 34.3 1.0
OG B:SER630 4.1 35.5 1.0
C5 B:3612 4.1 36.0 1.0
C10 B:3612 4.1 34.8 1.0
CZ B:ARG125 4.2 37.5 1.0
CD B:GLU205 4.4 32.6 1.0
C13 B:3612 4.6 34.2 1.0
F27 B:3612 4.8 34.9 1.0
O B:HOH794 4.8 44.1 1.0
CZ B:TYR662 4.9 31.6 1.0
CG B:HIS740 4.9 32.3 1.0
NH1 B:ARG125 5.0 37.4 1.0

Reference:

S.D.Edmondson, A.Mastracchio, J.M.Cox, G.J.Eiermann, H.He, K.A.Lyons, R.A.Patel, S.B.Patel, A.Petrov, G.Scapin, J.K.Wu, S.Xu, B.Zhu, N.A.Thornberry, R.S.Roy, A.E.Weber. Aminopiperidine-Fused Imidazoles As Dipeptidyl Peptidase-IV Inhibitors Bioorg.Med.Chem.Lett. V. 19 4097 2009.
ISSN: ISSN 0960-894X
PubMed: 19539471
DOI: 10.1016/J.BMCL.2009.06.011
Page generated: Wed Jul 31 19:10:05 2024

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