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Fluorine in PDB 3hab: The Structure of DPP4 in Complex with Piperidine Fused Benzimidazole 25

Enzymatic activity of The Structure of DPP4 in Complex with Piperidine Fused Benzimidazole 25

All present enzymatic activity of The Structure of DPP4 in Complex with Piperidine Fused Benzimidazole 25:
3.4.14.5;

Protein crystallography data

The structure of The Structure of DPP4 in Complex with Piperidine Fused Benzimidazole 25, PDB code: 3hab 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 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.908, 125.645, 136.941, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 21.1

Other elements in 3hab:

The structure of The Structure of DPP4 in Complex with Piperidine Fused Benzimidazole 25 also contains other interesting chemical elements:

Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The Structure of DPP4 in Complex with Piperidine Fused Benzimidazole 25 (pdb code 3hab). 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 DPP4 in Complex with Piperidine Fused Benzimidazole 25, PDB code: 3hab:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3hab

Go back to Fluorine Binding Sites List in 3hab
Fluorine binding site 1 out of 6 in the The Structure of DPP4 in Complex with Piperidine Fused Benzimidazole 25


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 DPP4 in Complex with Piperidine Fused Benzimidazole 25 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F767

b:18.7
occ:1.00
 F27 A:677767 0.0 18.7 1.0
C6 A:677767 1.3 18.2 1.0
C5 A:677767 2.4 17.2 1.0
C1 A:677767 2.4 17.6 1.0
F21 A:677767 2.7 17.7 1.0
CG2 A:VAL656 3.1 21.0 1.0
CG2 A:VAL711 3.2 22.8 1.0
OG A:SER630 3.5 27.2 1.0
C4 A:677767 3.6 15.4 1.0
C2 A:677767 3.6 17.1 1.0
N A:TYR631 3.8 24.1 1.0
C A:SER630 4.0 23.8 1.0
CE1 A:TYR662 4.0 23.6 1.0
CZ A:TYR662 4.1 22.6 1.0
C3 A:677767 4.2 17.3 1.0
CA A:SER630 4.3 23.7 1.0
OH A:TYR662 4.4 23.1 1.0
CA A:TYR631 4.4 23.9 1.0
CB A:VAL656 4.4 21.9 1.0
CD1 A:TYR662 4.5 22.6 1.0
CB A:SER630 4.5 23.3 1.0
O A:SER630 4.5 24.2 1.0
NE2 A:HIS740 4.6 22.5 1.0
CE2 A:TYR662 4.6 22.0 1.0
CB A:VAL711 4.7 22.3 1.0
F22 A:677767 4.7 17.5 1.0
CE1 A:HIS740 4.8 22.1 1.0
N A:VAL656 4.8 22.2 1.0
CB A:TYR631 4.8 23.5 1.0
CG A:TYR662 4.9 22.4 1.0
CD2 A:TYR662 5.0 22.6 1.0
CG1 A:VAL711 5.0 21.7 1.0

Fluorine binding site 2 out of 6 in 3hab

Go back to Fluorine Binding Sites List in 3hab
Fluorine binding site 2 out of 6 in the The Structure of DPP4 in Complex with Piperidine Fused Benzimidazole 25


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 DPP4 in Complex with Piperidine Fused Benzimidazole 25 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F767

b:17.5
occ:1.00
 F22 A:677767 0.0 17.5 1.0
C2 A:677767 1.3 17.1 1.0
C1 A:677767 2.3 17.6 1.0
C3 A:677767 2.4 17.3 1.0
C9 A:677767 2.8 17.0 1.0
NH2 A:ARG125 3.0 25.6 1.0
ND2 A:ASN710 3.0 21.7 1.0
OE2 A:GLU205 3.3 23.4 1.0
N23 A:677767 3.3 13.6 1.0
O A:HOH1223 3.4 26.0 1.0
C6 A:677767 3.6 18.2 1.0
C4 A:677767 3.6 15.4 1.0
O A:HOH848 3.6 17.8 1.0
OH A:TYR662 3.6 23.1 1.0
C14 A:677767 3.7 17.3 1.0
CG A:ASN710 3.8 23.4 1.0
CD2 A:HIS740 3.8 23.8 1.0
OD1 A:ASN710 3.9 26.8 1.0
NE2 A:HIS740 3.9 22.5 1.0
OG A:SER630 4.0 27.2 1.0
C5 A:677767 4.1 17.2 1.0
C10 A:677767 4.1 18.7 1.0
CZ A:ARG125 4.3 27.8 1.0
CD A:GLU205 4.5 23.7 1.0
C13 A:677767 4.7 17.5 1.0
F27 A:677767 4.7 18.7 1.0
CZ A:TYR662 4.8 22.6 1.0
CG A:HIS740 5.0 24.0 1.0

Fluorine binding site 3 out of 6 in 3hab

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Fluorine binding site 3 out of 6 in the The Structure of DPP4 in Complex with Piperidine Fused Benzimidazole 25


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 DPP4 in Complex with Piperidine Fused Benzimidazole 25 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F767

b:17.7
occ:1.00
 F21 A:677767 0.0 17.7 1.0
C5 A:677767 1.3 17.2 1.0
C6 A:677767 2.3 18.2 1.0
C4 A:677767 2.4 15.4 1.0
F27 A:677767 2.7 18.7 1.0
CD2 A:TYR631 3.3 23.2 1.0
CE1 A:TYR666 3.4 24.9 1.0
OH A:TYR666 3.5 25.0 1.0
CZ A:TYR666 3.5 26.0 1.0
C1 A:677767 3.6 17.6 1.0
C3 A:677767 3.6 17.3 1.0
CB A:TYR631 3.8 23.5 1.0
CH2 A:TRP659 4.0 21.0 1.0
CG A:TYR631 4.0 23.2 1.0
C2 A:677767 4.1 17.1 1.0
CA A:TYR631 4.2 23.9 1.0
CD1 A:TYR666 4.2 24.0 1.0
CZ3 A:TRP659 4.3 21.4 1.0
O A:HOH1005 4.3 24.7 1.0
CE2 A:TYR662 4.3 22.0 1.0
N A:TYR631 4.3 24.1 1.0
CE2 A:TYR666 4.3 26.6 1.0
CE2 A:TYR631 4.3 21.5 1.0
CG2 A:VAL656 4.4 21.0 1.0
OH A:TYR547 4.5 30.4 1.0
CZ A:TYR662 4.6 22.6 1.0
CD2 A:TYR662 4.7 22.6 1.0
OH A:TYR662 4.8 23.1 1.0
OG A:SER630 4.8 27.2 1.0
C9 A:677767 4.9 17.0 1.0
CG A:TYR666 4.9 24.8 1.0
CD2 A:TYR666 5.0 24.3 1.0

Fluorine binding site 4 out of 6 in 3hab

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Fluorine binding site 4 out of 6 in the The Structure of DPP4 in Complex with Piperidine Fused Benzimidazole 25


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 DPP4 in Complex with Piperidine Fused Benzimidazole 25 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:18.6
occ:1.00
 F27 B:6772 0.0 18.6 1.0
C6 B:6772 1.3 17.7 1.0
C5 B:6772 2.3 18.4 1.0
C1 B:6772 2.4 17.3 1.0
F21 B:6772 2.7 19.4 1.0
CG2 B:VAL711 3.1 21.0 1.0
CG2 B:VAL656 3.2 20.5 1.0
OG B:SER630 3.3 25.7 1.0
C4 B:6772 3.6 18.1 1.0
C2 B:6772 3.6 18.8 1.0
N B:TYR631 3.8 22.9 1.0
CE1 B:TYR662 4.0 21.4 1.0
CZ B:TYR662 4.0 23.1 1.0
C B:SER630 4.1 23.6 1.0
C3 B:6772 4.1 18.5 1.0
OH B:TYR662 4.2 23.2 1.0
CA B:SER630 4.4 23.7 1.0
CB B:SER630 4.4 24.1 1.0
CA B:TYR631 4.5 22.7 1.0
CD1 B:TYR662 4.5 22.8 1.0
CE2 B:TYR662 4.5 20.2 1.0
CB B:VAL656 4.5 21.8 1.0
NE2 B:HIS740 4.5 23.6 1.0
CB B:VAL711 4.6 21.6 1.0
O B:SER630 4.6 23.7 1.0
CE1 B:HIS740 4.7 24.0 1.0
F22 B:6772 4.7 15.6 1.0
CB B:TYR631 4.9 22.3 1.0
CD2 B:TYR662 4.9 21.5 1.0
N B:VAL656 4.9 21.5 1.0
CG B:TYR662 4.9 21.4 1.0
CG1 B:VAL711 5.0 20.6 1.0

Fluorine binding site 5 out of 6 in 3hab

Go back to Fluorine Binding Sites List in 3hab
Fluorine binding site 5 out of 6 in the The Structure of DPP4 in Complex with Piperidine Fused Benzimidazole 25


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 DPP4 in Complex with Piperidine Fused Benzimidazole 25 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:15.6
occ:1.00
 F22 B:6772 0.0 15.6 1.0
C2 B:6772 1.4 18.8 1.0
C1 B:6772 2.4 17.3 1.0
C3 B:6772 2.4 18.5 1.0
C9 B:6772 2.8 19.1 1.0
NH2 B:ARG125 3.0 26.8 1.0
ND2 B:ASN710 3.1 23.1 1.0
OE2 B:GLU205 3.2 26.9 1.0
N23 B:6772 3.4 16.0 1.0
O B:HOH830 3.5 33.5 1.0
C6 B:6772 3.6 17.7 1.0
OH B:TYR662 3.7 23.2 1.0
C4 B:6772 3.7 18.1 1.0
C14 B:6772 3.7 19.9 1.0
OD1 B:ASN710 3.7 26.4 1.0
CG B:ASN710 3.7 23.4 1.0
O B:HOH908 3.8 19.2 1.0
CD2 B:HIS740 3.9 24.4 1.0
NE2 B:HIS740 4.0 23.6 1.0
C10 B:6772 4.1 20.9 1.0
C5 B:6772 4.1 18.4 1.0
OG B:SER630 4.2 25.7 1.0
CZ B:ARG125 4.3 27.4 1.0
CD B:GLU205 4.4 25.6 1.0
O B:HOH967 4.4 44.2 1.0
C13 B:6772 4.6 20.8 1.0
F27 B:6772 4.7 18.6 1.0
CZ B:TYR662 4.8 23.1 1.0
CG B:HIS740 5.0 24.6 1.0

Fluorine binding site 6 out of 6 in 3hab

Go back to Fluorine Binding Sites List in 3hab
Fluorine binding site 6 out of 6 in the The Structure of DPP4 in Complex with Piperidine Fused Benzimidazole 25


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 DPP4 in Complex with Piperidine Fused Benzimidazole 25 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:19.4
occ:1.00
 F21 B:6772 0.0 19.4 1.0
C5 B:6772 1.3 18.4 1.0
C6 B:6772 2.4 17.7 1.0
C4 B:6772 2.4 18.1 1.0
F27 B:6772 2.7 18.6 1.0
CD2 B:TYR631 3.4 21.2 1.0
CE1 B:TYR666 3.4 25.1 1.0
OH B:TYR666 3.4 24.8 1.0
CZ B:TYR666 3.5 24.7 1.0
C1 B:6772 3.6 17.3 1.0
C3 B:6772 3.6 18.5 1.0
CB B:TYR631 3.8 22.3 1.0
CH2 B:TRP659 4.0 22.4 1.0
CG B:TYR631 4.1 22.2 1.0
C2 B:6772 4.1 18.8 1.0
CD1 B:TYR666 4.2 25.1 1.0
CE2 B:TYR662 4.2 20.2 1.0
CA B:TYR631 4.3 22.7 1.0
CZ3 B:TRP659 4.3 23.2 1.0
CE2 B:TYR666 4.3 24.5 1.0
N B:TYR631 4.4 22.9 1.0
O B:HOH1100 4.4 29.2 1.0
CE2 B:TYR631 4.5 21.9 1.0
CG2 B:VAL656 4.5 20.5 1.0
CZ B:TYR662 4.5 23.1 1.0
OH B:TYR547 4.6 28.9 1.0
CD2 B:TYR662 4.7 21.5 1.0
OG B:SER630 4.7 25.7 1.0
OH B:TYR662 4.7 23.2 1.0
C9 B:6772 4.9 19.1 1.0
CG B:TYR666 4.9 24.5 1.0
CD2 B:TYR666 4.9 23.8 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: Mon Jul 14 16:46:00 2025

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