Fluorine in PDB 8g6a: Wildtype PTP1B in Complex with DES6016

Enzymatic activity of Wildtype PTP1B in Complex with DES6016

All present enzymatic activity of Wildtype PTP1B in Complex with DES6016:
3.1.3.48;

Protein crystallography data

The structure of Wildtype PTP1B in Complex with DES6016, PDB code: 8g6a was solved by J.B.Greisman, L.Willmore, C.Y.Yeh, F.Giordanetto, S.Shahamadtar, H.Nisonoff, P.Maragakis, D.E.Shaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.95 / 1.62
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 88.35, 88.35, 162.66, 90, 90, 90
R / Rfree (%) 17.8 / 21.7

Other elements in 8g6a:

The structure of Wildtype PTP1B in Complex with DES6016 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Wildtype PTP1B in Complex with DES6016 (pdb code 8g6a). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Wildtype PTP1B in Complex with DES6016, PDB code: 8g6a:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8g6a

Go back to Fluorine Binding Sites List in 8g6a
Fluorine binding site 1 out of 6 in the Wildtype PTP1B in Complex with DES6016


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Wildtype PTP1B in Complex with DES6016 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:59.6
occ:1.00
 F16 A:ZD3301 0.0 59.6 1.0
C15 A:ZD3301 1.4 59.3 1.0
F17 A:ZD3301 2.1 63.5 1.0
F18 A:ZD3301 2.2 64.0 1.0
C7 A:ZD3301 2.4 61.7 1.0
C8 A:ZD3301 2.7 64.4 1.0
O A:LEU192 3.3 33.0 1.0
CD2 A:LEU192 3.5 32.2 1.0
N6 A:ZD3301 3.6 60.4 1.0
CD2 A:LEU195 4.0 32.3 1.0
CB A:LEU192 4.0 31.5 1.0
C A:LEU192 4.1 30.0 1.0
C9 A:ZD3301 4.1 65.5 1.0
CA A:LEU192 4.1 29.5 1.0
CD1 A:LEU232 4.2 37.0 1.0
N A:PHE196 4.2 32.2 1.0
CG A:LEU195 4.3 31.0 1.0
CB A:LEU195 4.3 30.7 1.0
CG A:LEU192 4.3 31.8 1.0
CB A:PHE196 4.4 40.3 1.0
CA A:PHE196 4.6 36.0 1.0
CB A:ZD3301 4.6 51.2 1.0
C5 A:ZD3301 4.7 65.4 1.0
N10 A:ZD3301 4.8 55.7 1.0
CA A:GLY277 4.8 38.7 1.0
C A:LEU195 4.9 30.9 1.0
C13 A:ZD3301 4.9 66.9 1.0

Fluorine binding site 2 out of 6 in 8g6a

Go back to Fluorine Binding Sites List in 8g6a
Fluorine binding site 2 out of 6 in the Wildtype PTP1B in Complex with DES6016


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Wildtype PTP1B in Complex with DES6016 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:63.5
occ:1.00
 F17 A:ZD3301 0.0 63.5 1.0
C15 A:ZD3301 1.3 59.3 1.0
F18 A:ZD3301 2.1 64.0 1.0
F16 A:ZD3301 2.1 59.6 1.0
C7 A:ZD3301 2.4 61.7 1.0
N6 A:ZD3301 2.8 60.4 1.0
NH1 A:ARG199 3.4 34.8 1.0
O A:HOH429 3.5 39.3 1.0
C8 A:ZD3301 3.5 64.4 1.0
CD1 A:LEU232 3.7 37.0 1.0
CD1 A:ILE281 3.7 74.5 1.0
CZ A:ARG199 3.8 35.1 1.0
NE A:ARG199 4.1 30.9 1.0
C5 A:ZD3301 4.1 65.4 1.0
CD2 A:LEU195 4.2 32.3 1.0
CD A:ARG199 4.2 31.7 1.0
NH2 A:ARG199 4.5 34.5 1.0
CG1 A:ILE281 4.6 74.9 1.0
CG A:LEU195 4.6 31.0 1.0
C9 A:ZD3301 4.7 65.5 1.0
CG A:LEU232 4.8 33.4 1.0
CB A:LEU232 4.9 32.8 1.0
C13 A:ZD3301 5.0 66.9 1.0
C4 A:ZD3301 5.0 61.8 1.0

Fluorine binding site 3 out of 6 in 8g6a

Go back to Fluorine Binding Sites List in 8g6a
Fluorine binding site 3 out of 6 in the Wildtype PTP1B in Complex with DES6016


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Wildtype PTP1B in Complex with DES6016 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:64.0
occ:1.00
 F18 A:ZD3301 0.0 64.0 1.0
C15 A:ZD3301 1.3 59.3 1.0
F17 A:ZD3301 2.1 63.5 1.0
F16 A:ZD3301 2.2 59.6 1.0
C7 A:ZD3301 2.3 61.7 1.0
CA A:PHE196 3.0 36.0 1.0
N6 A:ZD3301 3.1 60.4 1.0
N A:PHE196 3.1 32.2 1.0
C8 A:ZD3301 3.2 64.4 1.0
CB A:PHE196 3.2 40.3 1.0
O A:HOH429 3.6 39.3 1.0
CD A:ARG199 3.7 31.7 1.0
C A:LEU195 3.7 30.9 1.0
CG A:LEU195 3.8 31.0 1.0
O A:LEU192 3.9 33.0 1.0
CD1 A:PHE196 3.9 50.8 1.0
CG A:PHE196 4.0 47.2 1.0
O A:LEU195 4.1 32.1 1.0
CD2 A:LEU195 4.1 32.3 1.0
NE A:ARG199 4.2 30.9 1.0
CB A:LEU195 4.2 30.7 1.0
C5 A:ZD3301 4.3 65.4 1.0
NH1 A:ARG199 4.3 34.8 1.0
C9 A:ZD3301 4.4 65.5 1.0
C A:PHE196 4.5 34.9 1.0
CZ A:ARG199 4.5 35.1 1.0
CG A:ARG199 4.5 30.8 1.0
CA A:LEU195 4.6 29.1 1.0
C13 A:ZD3301 4.9 66.9 1.0
O A:PHE196 4.9 36.3 1.0
CB A:ARG199 4.9 32.8 1.0
C A:LEU192 5.0 30.0 1.0

Fluorine binding site 4 out of 6 in 8g6a

Go back to Fluorine Binding Sites List in 8g6a
Fluorine binding site 4 out of 6 in the Wildtype PTP1B in Complex with DES6016


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Wildtype PTP1B in Complex with DES6016 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:56.4
occ:1.00
 F16 A:ZD5302 0.0 56.4 1.0
C15 A:ZD5302 1.4 58.1 1.0
F18 A:ZD5302 2.2 47.0 1.0
F17 A:ZD5302 2.2 49.6 1.0
OD1 A:ASP265 2.4 61.0 1.0
C7 A:ZD5302 2.4 62.5 1.0
C8 A:ZD5302 2.8 79.1 1.0
CG A:ASP265 3.4 51.0 1.0
N6 A:ZD5302 3.6 58.0 1.0
O A:HOH511 3.9 37.8 1.0
CA A:ASP265 3.9 35.6 1.0
N A:ASP265 3.9 33.7 1.0
CB A:ASP265 4.1 41.2 1.0
C9 A:ZD5302 4.2 91.2 1.0
O A:HOH479 4.2 53.6 1.0
OD2 A:ASP265 4.3 55.5 1.0
C A:ALA264 4.5 31.2 1.0
CB A:ALA264 4.6 33.4 1.0
C5 A:ZD5302 4.7 80.7 1.0
O A:ALA264 4.9 30.6 1.0
N10 A:ZD5302 4.9 100.0 1.0
C13 A:ZD5302 5.0 89.9 1.0

Fluorine binding site 5 out of 6 in 8g6a

Go back to Fluorine Binding Sites List in 8g6a
Fluorine binding site 5 out of 6 in the Wildtype PTP1B in Complex with DES6016


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Wildtype PTP1B in Complex with DES6016 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:49.6
occ:1.00
 F17 A:ZD5302 0.0 49.6 1.0
C15 A:ZD5302 1.4 58.1 1.0
F16 A:ZD5302 2.2 56.4 1.0
F18 A:ZD5302 2.2 47.0 1.0
C7 A:ZD5302 2.5 62.5 1.0
N6 A:ZD5302 2.9 58.0 1.0
O A:HOH532 3.1 42.3 1.0
O A:HOH476 3.2 36.4 1.0
CB A:TRP16 3.5 30.8 1.0
C8 A:ZD5302 3.7 79.1 1.0
CG A:TRP16 4.1 30.3 1.0
CD1 A:TRP16 4.2 31.1 1.0
CB A:ALA264 4.2 33.4 1.0
C5 A:ZD5302 4.3 80.7 1.0
OD1 A:ASP265 4.6 61.0 1.0
N A:ALA17 4.6 33.4 1.0
CA A:TRP16 4.7 30.6 1.0
C9 A:ZD5302 4.9 91.2 1.0
C A:ALA264 4.9 31.2 1.0
N A:ASP265 4.9 33.7 1.0
C A:TRP16 4.9 31.0 1.0
N A:TRP16 4.9 32.2 1.0

Fluorine binding site 6 out of 6 in 8g6a

Go back to Fluorine Binding Sites List in 8g6a
Fluorine binding site 6 out of 6 in the Wildtype PTP1B in Complex with DES6016


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Wildtype PTP1B in Complex with DES6016 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:47.0
occ:1.00
 F18 A:ZD5302 0.0 47.0 1.0
C15 A:ZD5302 1.3 58.1 1.0
F16 A:ZD5302 2.2 56.4 1.0
F17 A:ZD5302 2.2 49.6 1.0
C7 A:ZD5302 2.3 62.5 1.0
N6 A:ZD5302 3.1 58.0 1.0
C8 A:ZD5302 3.1 79.1 1.0
CB A:TRP16 3.5 30.8 1.0
O A:ALA264 3.5 30.6 1.0
CA A:ASP265 3.6 35.6 1.0
N A:ASP265 3.6 33.7 1.0
C A:ALA264 3.6 31.2 1.0
CG A:TRP16 3.7 30.3 1.0
CD A:ARG268 3.7 33.2 1.0
CD1 A:TRP16 3.8 31.1 1.0
OD1 A:ASP265 3.8 61.0 1.0
CB A:ARG268 3.9 31.2 1.0
O A:HOH479 3.9 53.6 1.0
CB A:ALA264 4.2 33.4 1.0
C5 A:ZD5302 4.2 80.7 1.0
CG A:ASP265 4.3 51.0 1.0
C9 A:ZD5302 4.3 91.2 1.0
CG A:ARG268 4.4 32.3 1.0
CB A:ASP265 4.5 41.2 1.0
CA A:ALA264 4.5 31.0 1.0
O A:HOH532 4.6 42.3 1.0
CD2 A:TRP16 4.6 30.5 1.0
NE1 A:TRP16 4.7 31.1 1.0
C A:ASP265 4.8 32.6 1.0
C13 A:ZD5302 4.8 89.9 1.0
NE A:ARG268 4.9 33.3 1.0
CA A:TRP16 5.0 30.6 1.0
O A:HOH511 5.0 37.8 1.0

Reference:

J.B.Greisman, L.Willmore, C.Y.Yeh, F.Giordanetto, S.Shahamadtar, H.Nisonoff, P.Maragakis, D.E.Shaw. Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1B: From Molecular Dynamics Simulations to X-Ray Crystallography To Be Published.
Page generated: Fri Aug 2 19:41:13 2024

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