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Fluorine in PDB 4pnz: Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102)

Enzymatic activity of Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102)

All present enzymatic activity of Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102):
3.4.14.5;

Protein crystallography data

The structure of Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102), PDB code: 4pnz was solved by G.Scapin, Y.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.15 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.940, 125.777, 137.085, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 19.7

Other elements in 4pnz:

The structure of Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102) also contains other interesting chemical elements:

Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102) (pdb code 4pnz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102), PDB code: 4pnz:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4pnz

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Fluorine binding site 1 out of 6 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:22.3
occ:1.00
 F2 A:2VH802 0.0 22.3 1.0
C A:2VH802 1.4 21.4 1.0
C5 A:2VH802 2.3 20.8 1.0
C1 A:2VH802 2.4 18.0 1.0
F A:2VH802 2.7 22.0 1.0
CG2 A:VAL656 3.1 14.0 1.0
CG2 A:VAL711 3.2 14.6 1.0
OG A:SER630 3.4 26.2 1.0
C2 A:2VH802 3.6 17.7 1.0
C4 A:2VH802 3.6 18.1 1.0
N A:TYR631 3.8 13.0 1.0
C A:SER630 4.0 16.5 1.0
CE1 A:TYR662 4.1 14.8 1.0
C3 A:2VH802 4.1 19.4 1.0
CZ A:TYR662 4.2 16.0 1.0
CB A:VAL656 4.3 14.8 1.0
CA A:SER630 4.3 13.5 1.0
CB A:SER630 4.4 17.3 1.0
CA A:TYR631 4.4 13.5 1.0
OH A:TYR662 4.4 16.0 1.0
CD1 A:TYR662 4.5 15.9 1.0
O A:SER630 4.5 16.6 1.0
CB A:VAL711 4.6 14.7 1.0
CE2 A:TYR662 4.6 15.0 1.0
NE2 A:HIS740 4.7 17.7 1.0
F1 A:2VH802 4.7 18.6 1.0
N A:VAL656 4.8 12.1 1.0
CE1 A:HIS740 4.8 17.5 1.0
CG A:TYR662 4.9 14.4 1.0
CG1 A:VAL711 4.9 13.7 1.0
CB A:TYR631 4.9 14.0 1.0
CD2 A:TYR662 4.9 14.7 1.0

Fluorine binding site 2 out of 6 in 4pnz

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Fluorine binding site 2 out of 6 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:22.0
occ:1.00
 F A:2VH802 0.0 22.0 1.0
C5 A:2VH802 1.4 20.8 1.0
C A:2VH802 2.3 21.4 1.0
C4 A:2VH802 2.4 18.1 1.0
F2 A:2VH802 2.7 22.3 1.0
CD2 A:TYR631 3.4 14.3 1.0
CE1 A:TYR666 3.5 16.5 1.0
OH A:TYR666 3.6 17.2 1.0
C1 A:2VH802 3.6 18.0 1.0
C3 A:2VH802 3.6 19.4 1.0
CB A:TYR631 3.7 14.0 1.0
CZ A:TYR666 3.7 18.7 1.0
CH2 A:TRP659 3.9 16.2 1.0
CG A:TYR631 4.0 15.0 1.0
CA A:TYR631 4.0 13.5 1.0
C2 A:2VH802 4.0 17.7 1.0
N A:TYR631 4.1 13.0 1.0
CZ3 A:TRP659 4.3 15.8 1.0
CE2 A:TYR662 4.3 15.0 1.0
CD1 A:TYR666 4.3 16.8 1.0
CG2 A:VAL656 4.4 14.0 1.0
CE2 A:TYR631 4.4 15.7 1.0
OG A:SER630 4.6 26.2 1.0
CE2 A:TYR666 4.6 15.8 1.0
CZ A:TYR662 4.6 16.0 1.0
OH A:TYR547 4.7 25.5 1.0
CD2 A:TYR662 4.7 14.7 1.0
O A:HOH1082 4.8 28.1 1.0
OH A:TYR662 4.9 16.0 1.0
C6 A:2VH802 4.9 19.4 1.0
C A:SER630 5.0 16.5 1.0

Fluorine binding site 3 out of 6 in 4pnz

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Fluorine binding site 3 out of 6 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:18.6
occ:1.00
 F1 A:2VH802 0.0 18.6 1.0
C2 A:2VH802 1.3 17.7 1.0
C1 A:2VH802 2.3 18.0 1.0
C3 A:2VH802 2.3 19.4 1.0
C6 A:2VH802 2.8 19.4 1.0
NH2 A:ARG125 3.1 19.2 1.0
ND2 A:ASN710 3.2 14.9 1.0
OE2 A:GLU205 3.4 16.2 1.0
N A:2VH802 3.5 16.9 1.0
OH A:TYR662 3.5 16.0 1.0
O A:HOH1101 3.6 30.5 1.0
C A:2VH802 3.6 21.4 1.0
C4 A:2VH802 3.6 18.1 1.0
OD1 A:ASN710 3.6 17.8 1.0
CG A:ASN710 3.7 19.1 1.0
O A:HOH978 3.7 24.7 1.0
C10 A:2VH802 3.7 17.4 1.0
CD2 A:HIS740 3.8 18.7 1.0
NE2 A:HIS740 3.8 17.7 1.0
OG A:SER630 3.9 26.2 1.0
O A:2VH802 3.9 22.3 1.0
C5 A:2VH802 4.0 20.8 1.0
CZ A:ARG125 4.5 30.8 1.0
CD A:GLU205 4.6 22.5 1.0
F2 A:2VH802 4.7 22.3 1.0
CZ A:TYR662 4.7 16.0 1.0
C9 A:2VH802 4.8 19.5 1.0
C7 A:2VH802 4.8 18.9 1.0
CG A:HIS740 4.8 16.3 1.0
CE1 A:HIS740 4.9 17.5 1.0
CB A:ASN710 4.9 11.4 1.0

Fluorine binding site 4 out of 6 in 4pnz

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Fluorine binding site 4 out of 6 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:21.5
occ:1.00
 F2 B:2VH801 0.0 21.5 1.0
C B:2VH801 1.3 21.6 1.0
C5 B:2VH801 2.3 23.3 1.0
C1 B:2VH801 2.4 19.6 1.0
F B:2VH801 2.7 21.1 1.0
CG2 B:VAL656 3.0 15.6 1.0
CG2 B:VAL711 3.1 14.2 1.0
OG B:SER630 3.4 28.2 1.0
C2 B:2VH801 3.6 21.6 1.0
C4 B:2VH801 3.6 22.4 1.0
N B:TYR631 3.9 17.3 1.0
C B:SER630 4.1 20.2 1.0
CZ B:TYR662 4.1 16.7 1.0
CE1 B:TYR662 4.1 15.1 1.0
C3 B:2VH801 4.1 20.9 1.0
CB B:VAL656 4.3 16.1 1.0
CA B:SER630 4.4 17.8 1.0
OH B:TYR662 4.4 17.3 1.0
CB B:SER630 4.4 19.6 1.0
CD1 B:TYR662 4.5 15.8 1.0
CA B:TYR631 4.5 16.3 1.0
CE2 B:TYR662 4.5 16.4 1.0
CB B:VAL711 4.6 14.3 1.0
O B:SER630 4.6 18.3 1.0
NE2 B:HIS740 4.7 18.9 1.0
F1 B:2VH801 4.7 20.1 1.0
CE1 B:HIS740 4.8 18.8 1.0
N B:VAL656 4.8 14.6 1.0
CG B:TYR662 4.9 14.4 1.0
CD2 B:TYR662 4.9 15.7 1.0
CG1 B:VAL711 5.0 13.2 1.0
CB B:TYR631 5.0 16.3 1.0

Fluorine binding site 5 out of 6 in 4pnz

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Fluorine binding site 5 out of 6 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:21.1
occ:1.00
 F B:2VH801 0.0 21.1 1.0
C5 B:2VH801 1.3 23.3 1.0
C B:2VH801 2.3 21.6 1.0
C4 B:2VH801 2.3 22.4 1.0
F2 B:2VH801 2.7 21.5 1.0
CD2 B:TYR631 3.3 16.6 1.0
OH B:TYR666 3.5 23.2 1.0
CE1 B:TYR666 3.6 21.1 1.0
C1 B:2VH801 3.6 19.6 1.0
C3 B:2VH801 3.6 20.9 1.0
CZ B:TYR666 3.7 22.5 1.0
CB B:TYR631 3.7 16.3 1.0
CG B:TYR631 4.0 16.5 1.0
CH2 B:TRP659 4.0 17.5 1.0
C2 B:2VH801 4.0 21.6 1.0
CA B:TYR631 4.1 16.3 1.0
N B:TYR631 4.1 17.3 1.0
CD1 B:TYR666 4.4 18.3 1.0
CE2 B:TYR631 4.4 16.1 1.0
CZ3 B:TRP659 4.4 17.2 1.0
CE2 B:TYR662 4.4 16.4 1.0
CG2 B:VAL656 4.4 15.6 1.0
OG B:SER630 4.5 28.2 1.0
OH B:TYR547 4.5 28.3 1.0
CE2 B:TYR666 4.6 17.1 1.0
CZ B:TYR662 4.7 16.7 1.0
O B:HOH1022 4.7 30.2 1.0
CD2 B:TYR662 4.8 15.7 1.0
C6 B:2VH801 4.9 17.7 1.0
OH B:TYR662 4.9 17.3 1.0

Fluorine binding site 6 out of 6 in 4pnz

Go back to Fluorine Binding Sites List in 4pnz
Fluorine binding site 6 out of 6 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:20.1
occ:1.00
 F1 B:2VH801 0.0 20.1 1.0
C2 B:2VH801 1.4 21.6 1.0
C1 B:2VH801 2.3 19.6 1.0
C3 B:2VH801 2.4 20.9 1.0
C6 B:2VH801 2.8 17.7 1.0
ND2 B:ASN710 3.2 14.8 1.0
NH2 B:ARG125 3.2 23.0 1.0
OE2 B:GLU205 3.4 19.3 1.0
OD1 B:ASN710 3.4 18.4 1.0
N B:2VH801 3.5 17.8 1.0
O B:HOH1108 3.5 32.7 1.0
OH B:TYR662 3.5 17.3 1.0
CG B:ASN710 3.6 20.6 1.0
C B:2VH801 3.6 21.6 1.0
C4 B:2VH801 3.6 22.4 1.0
C10 B:2VH801 3.7 17.7 1.0
CD2 B:HIS740 3.8 19.2 1.0
O B:HOH1008 3.9 22.6 1.0
NE2 B:HIS740 3.9 18.9 1.0
O B:2VH801 4.0 20.1 1.0
OG B:SER630 4.0 28.2 1.0
C5 B:2VH801 4.1 23.3 1.0
CD B:GLU205 4.5 24.8 1.0
CZ B:ARG125 4.5 37.0 1.0
O B:HOH1619 4.5 48.0 1.0
CZ B:TYR662 4.6 16.7 1.0
F2 B:2VH801 4.7 21.5 1.0
C9 B:2VH801 4.7 17.7 1.0
CB B:ASN710 4.8 13.9 1.0
CG B:HIS740 4.8 17.4 1.0
C7 B:2VH801 4.8 18.7 1.0
CE1 B:HIS740 4.9 18.8 1.0

Reference:

T.Biftu, R.Sinha-Roy, P.Chen, X.Qian, D.Feng, J.T.Kuethe, G.Scapin, Y.D.Gao, Y.Yan, D.Krueger, A.Bak, G.Eiermann, J.He, J.Cox, J.Hicks, K.Lyons, H.He, G.Salituro, S.Tong, S.Patel, G.Doss, A.Petrov, J.Wu, S.S.Xu, C.Sewall, X.Zhang, B.Zhang, N.A.Thornberry, A.E.Weber. Omarigliptin (Mk-3102): A Novel Long-Acting Dpp-4 Inhibitor For Once-Weekly Treatment of Type 2 Diabetes. J.Med.Chem. V. 57 3205 2014.
ISSN: ISSN 0022-2623
PubMed: 24660890
DOI: 10.1021/JM401992E
Page generated: Sun Dec 13 12:10:52 2020

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