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Fluorine in PDB 7fqi: Crystal Structure of Human Legumain in Complex with (2S)-N-[(1S)-3- Amino-1-Cyano-3-Oxopropyl]-1-[1-[4-[(2,4-Difluorophenyl) Methoxy]Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2-Carboxamide

Enzymatic activity of Crystal Structure of Human Legumain in Complex with (2S)-N-[(1S)-3- Amino-1-Cyano-3-Oxopropyl]-1-[1-[4-[(2,4-Difluorophenyl) Methoxy]Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2-Carboxamide

All present enzymatic activity of Crystal Structure of Human Legumain in Complex with (2S)-N-[(1S)-3- Amino-1-Cyano-3-Oxopropyl]-1-[1-[4-[(2,4-Difluorophenyl) Methoxy]Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2-Carboxamide:
3.4.22.34;

Protein crystallography data

The structure of Crystal Structure of Human Legumain in Complex with (2S)-N-[(1S)-3- Amino-1-Cyano-3-Oxopropyl]-1-[1-[4-[(2,4-Difluorophenyl) Methoxy]Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2-Carboxamide, PDB code: 7fqi was solved by A.Ehler, J.Benz, B.Bartels, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.37 / 1.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 229.51, 67.093, 79.12, 90, 100.63, 90
R / Rfree (%) 16.7 / 18.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Legumain in Complex with (2S)-N-[(1S)-3- Amino-1-Cyano-3-Oxopropyl]-1-[1-[4-[(2,4-Difluorophenyl) Methoxy]Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2-Carboxamide (pdb code 7fqi). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of Human Legumain in Complex with (2S)-N-[(1S)-3- Amino-1-Cyano-3-Oxopropyl]-1-[1-[4-[(2,4-Difluorophenyl) Methoxy]Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2-Carboxamide, PDB code: 7fqi:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 7fqi

Go back to Fluorine Binding Sites List in 7fqi
Fluorine binding site 1 out of 8 in the Crystal Structure of Human Legumain in Complex with (2S)-N-[(1S)-3- Amino-1-Cyano-3-Oxopropyl]-1-[1-[4-[(2,4-Difluorophenyl) Methoxy]Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human Legumain in Complex with (2S)-N-[(1S)-3- Amino-1-Cyano-3-Oxopropyl]-1-[1-[4-[(2,4-Difluorophenyl) Methoxy]Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:26.3
occ:1.00
 F35 A:WSN501 0.0 26.3 1.0
C30 A:WSN501 1.3 21.2 1.0
C29 A:WSN501 2.3 21.1 1.0
C31 A:WSN501 2.3 22.2 1.0
CG2 C:THR264 3.1 16.1 1.0
CE2 A:TYR41 3.3 18.1 1.0
CD2 A:TYR41 3.3 16.6 1.0
CB C:THR264 3.5 15.4 1.0
C28 A:WSN501 3.6 21.7 1.0
C32 A:WSN501 3.6 20.8 1.0
CG C:TYR217 3.6 15.2 1.0
CZ A:TYR41 3.7 19.6 1.0
CD1 C:TYR217 3.7 17.7 1.0
CG A:TYR41 3.7 16.7 1.0
CD2 C:TYR217 3.9 16.0 1.0
O C:HOH745 4.0 40.8 1.0
CE1 A:TYR41 4.0 17.8 1.0
CD1 A:TYR41 4.0 17.9 1.0
CE1 C:TYR217 4.1 16.3 1.0
C27 A:WSN501 4.1 20.8 1.0
CB C:TYR217 4.1 15.3 1.0
CA C:THR264 4.2 15.6 1.0
CE2 C:TYR217 4.2 16.4 1.0
CZ C:TYR217 4.3 17.9 1.0
OH A:TYR41 4.4 21.4 1.0
O C:THR264 4.5 16.0 1.0
CB A:TYR41 4.6 14.9 1.0
F36 A:WSN501 4.7 23.2 1.0
OG1 C:THR264 4.8 14.9 1.0
C C:THR264 4.8 15.4 1.0

Fluorine binding site 2 out of 8 in 7fqi

Go back to Fluorine Binding Sites List in 7fqi
Fluorine binding site 2 out of 8 in the Crystal Structure of Human Legumain in Complex with (2S)-N-[(1S)-3- Amino-1-Cyano-3-Oxopropyl]-1-[1-[4-[(2,4-Difluorophenyl) Methoxy]Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human Legumain in Complex with (2S)-N-[(1S)-3- Amino-1-Cyano-3-Oxopropyl]-1-[1-[4-[(2,4-Difluorophenyl) Methoxy]Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:23.2
occ:1.00
 F36 A:WSN501 0.0 23.2 1.0
C28 A:WSN501 1.4 21.7 1.0
C27 A:WSN501 2.3 20.8 1.0
C29 A:WSN501 2.3 21.1 1.0
C26 A:WSN501 2.8 20.3 1.0
OH C:TYR217 3.0 19.8 1.0
C1 A:EDO504 3.0 31.5 1.0
O25 A:WSN501 3.2 16.3 1.0
C2 A:EDO504 3.3 35.5 1.0
O C:HOH729 3.4 17.7 1.0
CZ C:TYR217 3.5 17.9 1.0
C30 A:WSN501 3.6 21.2 1.0
C32 A:WSN501 3.6 20.8 1.0
O C:HOH687 3.8 18.8 1.0
CE2 C:TYR217 3.8 16.4 1.0
CB A:TYR41 3.9 14.9 1.0
O2 A:EDO504 4.0 34.5 1.0
C31 A:WSN501 4.1 22.2 1.0
C22 A:WSN501 4.4 15.3 1.0
O1 A:EDO504 4.4 25.1 1.0
C1 A:EDO503 4.4 23.2 1.0
O C:THR264 4.4 16.0 1.0
CE1 C:TYR217 4.5 16.3 1.0
CG A:TYR41 4.7 16.7 1.0
F35 A:WSN501 4.7 26.3 1.0
O C:HOH673 4.7 31.6 1.0
CD2 C:TYR217 4.9 16.0 1.0

Fluorine binding site 3 out of 8 in 7fqi

Go back to Fluorine Binding Sites List in 7fqi
Fluorine binding site 3 out of 8 in the Crystal Structure of Human Legumain in Complex with (2S)-N-[(1S)-3- Amino-1-Cyano-3-Oxopropyl]-1-[1-[4-[(2,4-Difluorophenyl) Methoxy]Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human Legumain in Complex with (2S)-N-[(1S)-3- Amino-1-Cyano-3-Oxopropyl]-1-[1-[4-[(2,4-Difluorophenyl) Methoxy]Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:34.5
occ:0.50
 F35 B:WSN501 0.0 34.5 0.5
F35 B:WSN501 0.9 27.6 0.5
C30 B:WSN501 1.4 32.3 0.5
C30 B:WSN501 1.5 26.6 0.5
C29 B:WSN501 1.9 26.3 0.5
C31 B:WSN501 2.3 30.5 0.5
C29 B:WSN501 2.3 31.9 0.5
C31 B:WSN501 2.7 27.0 0.5
C28 B:WSN501 3.3 27.3 0.5
C28 B:WSN501 3.6 33.5 0.5
C32 B:WSN501 3.6 32.4 0.5
C32 B:WSN501 3.8 28.9 0.5
C27 B:WSN501 4.0 28.6 0.5
C27 B:WSN501 4.1 33.0 0.5
F36 B:WSN501 4.2 27.6 0.5
CD2 B:TYR41 4.5 23.4 0.5
CD2 B:TYR41 4.6 28.0 0.5
F36 B:WSN501 4.7 38.8 0.5
CE2 B:TYR41 4.8 22.9 0.5
CG B:TYR41 4.9 23.4 0.5
CE2 B:TYR41 4.9 25.3 0.5
CG B:TYR41 5.0 24.2 0.5

Fluorine binding site 4 out of 8 in 7fqi

Go back to Fluorine Binding Sites List in 7fqi
Fluorine binding site 4 out of 8 in the Crystal Structure of Human Legumain in Complex with (2S)-N-[(1S)-3- Amino-1-Cyano-3-Oxopropyl]-1-[1-[4-[(2,4-Difluorophenyl) Methoxy]Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human Legumain in Complex with (2S)-N-[(1S)-3- Amino-1-Cyano-3-Oxopropyl]-1-[1-[4-[(2,4-Difluorophenyl) Methoxy]Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:27.6
occ:0.50
 F35 B:WSN501 0.0 27.6 0.5
F35 B:WSN501 0.9 34.5 0.5
C30 B:WSN501 1.4 26.6 0.5
C30 B:WSN501 1.6 32.3 0.5
C29 B:WSN501 2.2 31.9 0.5
C31 B:WSN501 2.3 27.0 0.5
C29 B:WSN501 2.4 26.3 0.5
C31 B:WSN501 2.9 30.5 0.5
C28 B:WSN501 3.5 33.5 0.5
C28 B:WSN501 3.6 27.3 0.5
C32 B:WSN501 3.6 28.9 0.5
C32 B:WSN501 4.0 32.4 0.5
C27 B:WSN501 4.1 28.6 0.5
C27 B:WSN501 4.2 33.0 0.5
CD2 B:TYR41 4.2 28.0 0.5
CE2 B:TYR41 4.4 25.3 0.5
F36 B:WSN501 4.4 38.8 0.5
F36 B:WSN501 4.7 27.6 0.5
CD2 B:TYR41 4.7 23.4 0.5
CG B:TYR41 4.8 24.2 0.5
CZ B:TYR41 5.0 26.9 0.5

Fluorine binding site 5 out of 8 in 7fqi

Go back to Fluorine Binding Sites List in 7fqi
Fluorine binding site 5 out of 8 in the Crystal Structure of Human Legumain in Complex with (2S)-N-[(1S)-3- Amino-1-Cyano-3-Oxopropyl]-1-[1-[4-[(2,4-Difluorophenyl) Methoxy]Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Human Legumain in Complex with (2S)-N-[(1S)-3- Amino-1-Cyano-3-Oxopropyl]-1-[1-[4-[(2,4-Difluorophenyl) Methoxy]Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:38.8
occ:0.50
 F36 B:WSN501 0.0 38.8 0.5
C32 B:WSN501 1.0 28.9 0.5
C28 B:WSN501 1.4 33.5 0.5
C27 B:WSN501 1.9 28.6 0.5
C31 B:WSN501 2.1 27.0 0.5
C27 B:WSN501 2.3 33.0 0.5
C29 B:WSN501 2.3 31.9 0.5
C26 B:WSN501 2.4 29.6 0.5
C26 B:WSN501 2.8 31.4 0.5
C28 B:WSN501 3.1 27.3 0.5
C30 B:WSN501 3.3 26.6 0.5
O B:HOH785 3.5 29.9 1.0
O25 B:WSN501 3.6 29.2 1.0
C30 B:WSN501 3.6 32.3 0.5
C32 B:WSN501 3.6 32.4 0.5
O B:HOH778 3.6 29.7 1.0
CE1 B:TYR41 3.6 27.4 0.5
C29 B:WSN501 3.7 26.3 0.5
CD1 B:TYR41 3.8 25.6 0.5
C31 B:WSN501 4.1 30.5 0.5
F36 B:WSN501 4.2 27.6 0.5
CZ B:TYR41 4.2 26.9 0.5
O B:HOH683 4.4 25.1 1.0
F35 B:WSN501 4.4 27.6 0.5
C22 B:WSN501 4.5 25.6 1.0
CG B:TYR41 4.6 24.2 0.5
F35 B:WSN501 4.7 34.5 0.5
OH B:TYR41 4.7 27.0 0.5
CE2 B:TYR41 4.9 25.3 0.5
O B:HOH601 4.9 12.7 0.5
CD2 B:TYR41 5.0 28.0 0.5
C21 B:WSN501 5.0 24.1 1.0

Fluorine binding site 6 out of 8 in 7fqi

Go back to Fluorine Binding Sites List in 7fqi
Fluorine binding site 6 out of 8 in the Crystal Structure of Human Legumain in Complex with (2S)-N-[(1S)-3- Amino-1-Cyano-3-Oxopropyl]-1-[1-[4-[(2,4-Difluorophenyl) Methoxy]Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Human Legumain in Complex with (2S)-N-[(1S)-3- Amino-1-Cyano-3-Oxopropyl]-1-[1-[4-[(2,4-Difluorophenyl) Methoxy]Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:27.6
occ:0.50
 F36 B:WSN501 0.0 27.6 0.5
C32 B:WSN501 0.9 32.4 0.5
C28 B:WSN501 1.4 27.3 0.5
C31 B:WSN501 1.9 30.5 0.5
C27 B:WSN501 1.9 33.0 0.5
C29 B:WSN501 2.3 26.3 0.5
C27 B:WSN501 2.4 28.6 0.5
C26 B:WSN501 2.7 31.4 0.5
O25 B:WSN501 2.9 29.2 1.0
C26 B:WSN501 2.9 29.6 0.5
C30 B:WSN501 3.1 32.3 0.5
C28 B:WSN501 3.1 33.5 0.5
C29 B:WSN501 3.6 31.9 0.5
C30 B:WSN501 3.6 26.6 0.5
CB B:TYR41 3.6 22.4 0.5
C32 B:WSN501 3.6 28.9 0.5
CG B:TYR41 3.7 23.4 0.5
CD1 B:TYR41 3.7 24.0 0.5
CB B:TYR41 3.8 23.1 0.5
O B:HOH733 3.9 27.4 1.0
C31 B:WSN501 4.1 27.0 0.5
C22 B:WSN501 4.1 25.6 1.0
F35 B:WSN501 4.2 34.5 0.5
F36 B:WSN501 4.2 38.8 0.5
CG B:TYR41 4.4 24.2 0.5
O B:HOH778 4.4 29.7 1.0
CE1 B:TYR41 4.6 24.5 0.5
CD2 B:TYR41 4.6 23.4 0.5
CD1 B:TYR41 4.6 25.6 0.5
F35 B:WSN501 4.7 27.6 0.5
CA B:TYR41 4.8 22.0 0.5
CA B:TYR41 4.8 21.8 0.5
C23 B:WSN501 4.9 23.6 1.0
C21 B:WSN501 5.0 24.1 1.0

Fluorine binding site 7 out of 8 in 7fqi

Go back to Fluorine Binding Sites List in 7fqi
Fluorine binding site 7 out of 8 in the Crystal Structure of Human Legumain in Complex with (2S)-N-[(1S)-3- Amino-1-Cyano-3-Oxopropyl]-1-[1-[4-[(2,4-Difluorophenyl) Methoxy]Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Human Legumain in Complex with (2S)-N-[(1S)-3- Amino-1-Cyano-3-Oxopropyl]-1-[1-[4-[(2,4-Difluorophenyl) Methoxy]Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:30.8
occ:1.00
 F35 C:WSN501 0.0 30.8 1.0
C30 C:WSN501 1.4 26.9 1.0
C31 C:WSN501 2.3 28.4 1.0
C29 C:WSN501 2.3 22.3 1.0
C28 C:WSN501 3.6 23.4 1.0
C32 C:WSN501 3.6 25.5 1.0
O C:HOH769 3.7 36.7 1.0
C27 C:WSN501 4.1 23.2 1.0
CD2 C:TYR41 4.6 18.6 1.0
F36 C:WSN501 4.7 27.8 1.0
CB C:TYR41 4.9 17.6 1.0
CG C:TYR41 4.9 17.4 1.0

Fluorine binding site 8 out of 8 in 7fqi

Go back to Fluorine Binding Sites List in 7fqi
Fluorine binding site 8 out of 8 in the Crystal Structure of Human Legumain in Complex with (2S)-N-[(1S)-3- Amino-1-Cyano-3-Oxopropyl]-1-[1-[4-[(2,4-Difluorophenyl) Methoxy]Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Human Legumain in Complex with (2S)-N-[(1S)-3- Amino-1-Cyano-3-Oxopropyl]-1-[1-[4-[(2,4-Difluorophenyl) Methoxy]Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:27.8
occ:1.00
 F36 C:WSN501 0.0 27.8 1.0
C28 C:WSN501 1.3 23.4 1.0
C27 C:WSN501 2.3 23.2 1.0
C29 C:WSN501 2.3 22.3 1.0
C26 C:WSN501 2.7 23.9 1.0
CB C:TYR41 3.5 17.6 1.0
CD1 C:TYR41 3.5 16.8 1.0
C30 C:WSN501 3.6 26.9 1.0
C32 C:WSN501 3.6 25.5 1.0
CG C:TYR41 3.6 17.4 1.0
O C:HOH665 3.9 17.4 1.0
O25 C:WSN501 4.0 22.3 1.0
C31 C:WSN501 4.1 28.4 1.0
CE1 C:TYR41 4.5 17.4 1.0
CD2 C:TYR41 4.6 18.6 1.0
F35 C:WSN501 4.7 30.8 1.0
CA C:TYR41 4.8 15.8 1.0
C22 C:WSN501 4.9 19.8 1.0
O C:TYR41 4.9 17.7 1.0

Reference:

B.Bartels, B.Kuhn, J.Benz, M.G.Rudolph. Crystal Structure of A Human Legumain Complex To Be Published.
Page generated: Fri Aug 2 07:07:22 2024

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