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Fluorine in PDB 4igs: Crystal Structure of Human Aldose Reductase Complexed with Nadp+ and JF0064

Enzymatic activity of Crystal Structure of Human Aldose Reductase Complexed with Nadp+ and JF0064

All present enzymatic activity of Crystal Structure of Human Aldose Reductase Complexed with Nadp+ and JF0064:
1.1.1.21;

Protein crystallography data

The structure of Crystal Structure of Human Aldose Reductase Complexed with Nadp+ and JF0064, PDB code: 4igs was solved by A.Cousido-Siah, F.X.Ruiz, A.Mitschler, S.Porte, A.R.De Lera, M.J.Martin, J.A.De La Fuente, G.Klebe, J.Farres, X.Pares, A.Podjarny, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.86 / 0.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.536, 66.880, 47.525, 90.00, 91.66, 90.00
R / Rfree (%) 13.5 / 14.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Aldose Reductase Complexed with Nadp+ and JF0064 (pdb code 4igs). 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 Aldose Reductase Complexed with Nadp+ and JF0064, PDB code: 4igs:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 4igs

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Fluorine binding site 1 out of 8 in the Crystal Structure of Human Aldose Reductase Complexed with Nadp+ and JF0064


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 Aldose Reductase Complexed with Nadp+ and JF0064 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:12.1
occ:0.79
 F15 A:64I402 0.0 12.1 0.8
C8 A:64I402 1.3 10.6 0.8
C10 A:64I402 2.3 10.9 0.8
C7 A:64I402 2.4 8.7 0.8
F14 A:64I402 2.7 12.4 0.8
O A:HOH986 2.8 28.8 0.3
C2 A:64I402 2.9 7.9 0.8
O A:HOH986 3.0 28.9 0.4
F22 A:64I402 3.1 8.9 0.8
C4 A:64I402 3.2 7.6 0.8
O A:HOH765 3.3 20.2 1.0
O A:HOH986 3.3 29.0 0.2
C9 A:64I402 3.6 8.0 0.8
O A:HOH937 3.6 28.9 1.0
C12 A:64I402 3.6 9.6 0.8
C1 A:64I402 3.8 7.8 0.8
C11 A:64I402 4.1 8.3 0.8
F18 A:64I402 4.3 9.1 0.8
C6 A:64I402 4.4 6.4 0.8
CZ A:PHE122 4.6 7.8 1.0
CD1 A:LEU300 4.6 11.3 1.0
O A:HOH1136 4.7 28.8 1.0
F16 A:64I402 4.7 8.1 0.8
CE1 A:PHE122 4.7 7.5 1.0
O13 A:64I402 4.7 10.0 0.8
CZ3 A:TRP219 4.8 11.1 1.0
C3 A:64I402 4.9 6.6 0.8
CZ2 A:TRP20 4.9 10.3 1.0

Fluorine binding site 2 out of 8 in 4igs

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Fluorine binding site 2 out of 8 in the Crystal Structure of Human Aldose Reductase Complexed with Nadp+ and JF0064


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 Aldose Reductase Complexed with Nadp+ and JF0064 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:12.4
occ:0.79
 F14 A:64I402 0.0 12.4 0.8
C10 A:64I402 1.3 10.9 0.8
C8 A:64I402 2.4 10.6 0.8
C12 A:64I402 2.4 9.6 0.8
F15 A:64I402 2.7 12.1 0.8
O13 A:64I402 2.8 10.0 0.8
O A:HOH1136 3.2 28.8 1.0
O A:HOH944 3.4 30.7 1.0
O A:HOH683 3.6 19.1 1.0
C11 A:64I402 3.6 8.3 0.8
C7 A:64I402 3.7 8.7 0.8
O A:HOH649 3.8 17.6 1.0
O A:HOH972 3.8 31.2 1.0
C9 A:64I402 4.1 8.0 0.8
O A:HOH816 4.3 15.0 1.0
O A:HOH986 4.4 28.8 0.3
CD1 A:LEU300 4.4 11.3 1.0
CZ3 A:TRP219 4.4 11.1 1.0
O A:HOH760 4.6 20.5 1.0
F17 A:64I402 4.7 7.9 0.8
CE3 A:TRP219 4.8 10.5 1.0
CZ A:PHE122 4.8 7.8 1.0
C2 A:64I402 4.9 7.9 0.8

Fluorine binding site 3 out of 8 in 4igs

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Fluorine binding site 3 out of 8 in the Crystal Structure of Human Aldose Reductase Complexed with Nadp+ and JF0064


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 Aldose Reductase Complexed with Nadp+ and JF0064 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:7.9
occ:0.79
 F17 A:64I402 0.0 7.9 0.8
C11 A:64I402 1.4 8.3 0.8
C9 A:64I402 2.4 8.0 0.8
C12 A:64I402 2.4 9.6 0.8
F16 A:64I402 2.6 8.1 0.8
O13 A:64I402 2.8 10.0 0.8
N A:LEU300 3.0 8.2 1.0
O A:HOH585 3.1 10.7 1.0
O A:HOH565 3.1 11.2 1.0
N A:ALA299 3.3 7.2 1.0
CZ2 A:TRP219 3.5 9.9 1.0
CA A:CYS298 3.5 6.7 0.6
CA A:LEU300 3.5 9.1 1.0
CA A:CYS298 3.5 7.5 0.4
C10 A:64I402 3.6 10.9 0.8
C A:CYS298 3.6 6.6 1.0
CH2 A:TRP219 3.7 10.9 1.0
C7 A:64I402 3.7 8.7 0.8
CE2 A:TRP219 4.0 8.9 1.0
C A:ALA299 4.0 7.8 1.0
C8 A:64I402 4.1 10.6 0.8
O A:VAL297 4.1 8.6 0.8
O A:VAL297 4.1 8.1 0.2
CB A:CYS298 4.2 6.5 0.6
CA A:ALA299 4.2 7.7 1.0
CZ3 A:TRP219 4.3 11.1 1.0
CB A:CYS298 4.3 8.8 0.4
CB A:LEU300 4.4 9.9 1.0
O A:CYS298 4.5 7.2 1.0
CD2 A:TRP219 4.6 9.3 1.0
SG A:CYS298 4.6 10.2 0.4
NE1 A:TRP219 4.6 8.8 1.0
N A:CYS298 4.6 7.2 1.0
CD1 A:LEU300 4.6 11.3 1.0
CE3 A:TRP219 4.7 10.5 1.0
C A:LEU300 4.7 9.2 1.0
N A:LEU301 4.7 9.7 1.0
F14 A:64I402 4.7 12.4 0.8
C A:VAL297 4.8 7.8 0.8
C A:VAL297 4.8 8.1 0.2
SG A:CYS298 4.8 6.2 0.6
C2 A:64I402 4.9 7.9 0.8
O A:HOH649 4.9 17.6 1.0

Fluorine binding site 4 out of 8 in 4igs

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Fluorine binding site 4 out of 8 in the Crystal Structure of Human Aldose Reductase Complexed with Nadp+ and JF0064


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 Aldose Reductase Complexed with Nadp+ and JF0064 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:8.1
occ:0.79
 F16 A:64I402 0.0 8.1 0.8
C9 A:64I402 1.3 8.0 0.8
C11 A:64I402 2.3 8.3 0.8
C7 A:64I402 2.3 8.7 0.8
F17 A:64I402 2.6 7.9 0.8
SG A:CYS298 2.8 10.2 0.4
C2 A:64I402 2.8 7.9 0.8
CB A:CYS298 3.0 6.5 0.6
CB A:CYS298 3.1 8.8 0.4
F18 A:64I402 3.2 9.1 0.8
C1 A:64I402 3.2 7.8 0.8
SG A:CYS298 3.4 6.2 0.6
CA A:CYS298 3.4 6.7 0.6
CA A:CYS298 3.4 7.5 0.4
C8 A:64I402 3.6 10.6 0.8
C12 A:64I402 3.6 9.6 0.8
C4 A:64I402 3.8 7.6 0.8
CH2 A:TRP219 3.8 10.9 1.0
C A:CYS298 3.9 6.6 1.0
C10 A:64I402 4.1 10.9 0.8
CZ2 A:TRP219 4.1 9.9 1.0
F22 A:64I402 4.2 8.9 0.8
O A:CYS298 4.3 7.2 1.0
CZ2 A:TRP111 4.3 7.2 1.0
C3 A:64I402 4.4 6.6 0.8
N A:ALA299 4.5 7.2 1.0
N A:LEU300 4.5 8.2 1.0
CH2 A:TRP111 4.6 7.7 1.0
O13 A:64I402 4.7 10.0 0.8
F15 A:64I402 4.7 12.1 0.8
C6 A:64I402 4.7 6.4 0.8
N A:CYS298 4.7 7.2 1.0
CZ3 A:TRP219 4.8 11.1 1.0
CD1 A:LEU300 4.8 11.3 1.0
CA A:LEU300 4.9 9.1 1.0

Fluorine binding site 5 out of 8 in 4igs

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Fluorine binding site 5 out of 8 in the Crystal Structure of Human Aldose Reductase Complexed with Nadp+ and JF0064


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 Aldose Reductase Complexed with Nadp+ and JF0064 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:8.9
occ:0.79
 F22 A:64I402 0.0 8.9 0.8
C4 A:64I402 1.3 7.6 0.8
C6 A:64I402 2.3 6.4 0.8
C2 A:64I402 2.4 7.9 0.8
F21 A:64I402 2.6 7.0 0.8
C7 A:64I402 2.8 8.7 0.8
O A:HOH986 2.9 28.9 0.4
F15 A:64I402 3.1 12.1 0.8
C8 A:64I402 3.2 10.6 0.8
NE1 A:TRP111 3.5 6.2 1.0
C1 A:64I402 3.6 7.8 0.8
CD1 A:LEU300 3.6 11.3 1.0
C5 A:64I402 3.6 5.6 0.8
C9 A:64I402 3.8 8.0 0.8
CZ2 A:TRP111 3.8 7.2 1.0
CH2 A:TRP79 3.8 5.6 1.0
CE2 A:TRP111 3.9 6.3 1.0
C3 A:64I402 4.1 6.6 0.8
O A:HOH937 4.2 28.9 1.0
F16 A:64I402 4.2 8.1 0.8
C10 A:64I402 4.3 10.9 0.8
CZ3 A:TRP79 4.3 5.3 1.0
CZ A:PHE122 4.4 7.8 1.0
O A:HOH986 4.4 29.0 0.2
CD1 A:TRP111 4.6 5.7 1.0
O A:HOH986 4.6 28.8 0.3
C11 A:64I402 4.7 8.3 0.8
F18 A:64I402 4.7 9.1 0.8
O20 A:64I402 4.7 4.8 0.8
CG A:LEU300 4.8 10.7 1.0
CH2 A:TRP111 4.9 7.7 1.0
CD2 A:LEU300 4.9 11.3 1.0
CZ2 A:TRP79 4.9 5.5 1.0
C12 A:64I402 5.0 9.6 0.8

Fluorine binding site 6 out of 8 in 4igs

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Fluorine binding site 6 out of 8 in the Crystal Structure of Human Aldose Reductase Complexed with Nadp+ and JF0064


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 Aldose Reductase Complexed with Nadp+ and JF0064 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:9.1
occ:0.79
 F18 A:64I402 0.0 9.1 0.8
C1 A:64I402 1.3 7.8 0.8
C2 A:64I402 2.3 7.9 0.8
C3 A:64I402 2.4 6.6 0.8
F19 A:64I402 2.7 7.4 0.8
C7 A:64I402 2.8 8.7 0.8
CH2 A:TRP20 2.9 11.4 1.0
CZ2 A:TRP20 3.1 10.3 1.0
CZ3 A:TRP20 3.1 11.6 1.0
F16 A:64I402 3.2 8.1 0.8
C9 A:64I402 3.2 8.0 0.8
CE2 A:TRP20 3.4 8.8 1.0
SG A:CYS298 3.4 10.2 0.4
CE3 A:TRP20 3.5 10.6 1.0
CH2 A:TRP219 3.6 10.9 1.0
C4 A:64I402 3.6 7.6 0.8
CD2 A:TRP20 3.6 8.3 1.0
C5 A:64I402 3.6 5.6 0.8
C8 A:64I402 3.8 10.6 0.8
SG A:CYS298 3.9 6.2 0.6
C6 A:64I402 4.1 6.4 0.8
C5N A:NAP401 4.2 4.7 1.0
NE1 A:TRP20 4.3 8.5 1.0
F15 A:64I402 4.3 12.1 0.8
CZ3 A:TRP219 4.3 11.1 1.0
C4N A:NAP401 4.4 4.8 1.0
C11 A:64I402 4.4 8.3 0.8
CZ2 A:TRP219 4.5 9.9 1.0
CG A:TRP20 4.6 6.4 1.0
O A:HOH937 4.6 28.9 1.0
F22 A:64I402 4.7 8.9 0.8
O20 A:64I402 4.7 4.8 0.8
CB A:CYS298 4.8 6.5 0.6
C10 A:64I402 4.9 10.9 0.8
CD1 A:TRP20 4.9 7.8 1.0

Fluorine binding site 7 out of 8 in 4igs

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Fluorine binding site 7 out of 8 in the Crystal Structure of Human Aldose Reductase Complexed with Nadp+ and JF0064


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 Aldose Reductase Complexed with Nadp+ and JF0064 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:7.4
occ:0.79
 F19 A:64I402 0.0 7.4 0.8
C3 A:64I402 1.3 6.6 0.8
C5 A:64I402 2.4 5.6 0.8
C1 A:64I402 2.4 7.8 0.8
F18 A:64I402 2.7 9.1 0.8
O20 A:64I402 2.7 4.8 0.8
C5N A:NAP401 2.9 4.7 1.0
C4N A:NAP401 3.0 4.8 1.0
CD2 A:TRP20 3.1 8.3 1.0
CE3 A:TRP20 3.2 10.6 1.0
C6N A:NAP401 3.3 4.4 1.0
CG A:TRP20 3.3 6.4 1.0
C3N A:NAP401 3.6 4.4 1.0
C6 A:64I402 3.6 6.4 0.8
C2 A:64I402 3.7 7.9 0.8
CE2 A:TRP20 3.7 8.8 1.0
CB A:TRP20 3.7 5.0 1.0
N1N A:NAP401 3.8 4.1 1.0
OH A:TYR48 3.8 4.9 1.0
C2N A:NAP401 3.9 4.1 1.0
CZ3 A:TRP20 3.9 11.6 1.0
CD1 A:TRP20 4.0 7.8 1.0
CE1 A:TYR48 4.1 4.8 1.0
C4 A:64I402 4.1 7.6 0.8
NE1 A:TRP20 4.2 8.5 1.0
CZ A:TYR48 4.2 4.5 1.0
CZ2 A:TRP20 4.4 10.3 1.0
O A:HOH937 4.4 28.9 1.0
CH2 A:TRP20 4.4 11.4 1.0
C7N A:NAP401 4.5 4.7 1.0
O7N A:NAP401 4.7 5.0 1.0
C2D A:NAP401 4.7 3.9 1.0
SG A:CYS298 4.7 10.2 0.4
F21 A:64I402 4.7 7.0 0.8
C1D A:NAP401 4.8 3.9 1.0
C7 A:64I402 4.9 8.7 0.8
C3D A:NAP401 5.0 3.8 1.0

Fluorine binding site 8 out of 8 in 4igs

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Fluorine binding site 8 out of 8 in the Crystal Structure of Human Aldose Reductase Complexed with Nadp+ and JF0064


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 Aldose Reductase Complexed with Nadp+ and JF0064 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:7.0
occ:0.79
 F21 A:64I402 0.0 7.0 0.8
C6 A:64I402 1.4 6.4 0.8
C4 A:64I402 2.3 7.6 0.8
C5 A:64I402 2.4 5.6 0.8
F22 A:64I402 2.6 8.9 0.8
NE2 A:HIS110 2.8 4.7 1.0
O20 A:64I402 2.8 4.8 0.8
NE1 A:TRP111 3.0 6.2 1.0
CE1 A:HIS110 3.2 4.5 1.0
CZ3 A:TRP79 3.2 5.3 1.0
CD2 A:HIS110 3.3 4.5 1.0
O A:HOH986 3.5 28.9 0.4
C3 A:64I402 3.6 6.6 0.8
C2 A:64I402 3.6 7.9 0.8
CH2 A:TRP79 3.8 5.6 1.0
CD1 A:TRP111 3.9 5.7 1.0
O7N A:NAP401 3.9 5.0 1.0
ND1 A:HIS110 3.9 4.1 1.0
CE2 A:TRP111 4.0 6.3 1.0
CG A:HIS110 4.0 4.0 1.0
C1 A:64I402 4.1 7.8 0.8
O A:HOH937 4.1 28.9 1.0
CG1 A:VAL47 4.2 5.5 1.0
CE3 A:TRP79 4.3 4.8 1.0
CZ2 A:TRP111 4.3 7.2 1.0
C7N A:NAP401 4.6 4.7 1.0
F19 A:64I402 4.7 7.4 0.8
CE1 A:TYR48 4.8 4.8 1.0
C7 A:64I402 4.8 8.7 0.8
O A:HOH986 4.9 29.0 0.2

Reference:

A.Cousido-Siah, F.X.Ruiz, A.Mitschler, S.Porte, A.R.De Lera, M.J.Martin, S.Manzanaro, J.A.De La Fuente, F.Terwesten, M.Betz, G.Klebe, J.Farres, X.Pares, A.Podjarny. Identification of A Novel Polyfluorinated Compound As A Lead to Inhibit the Human Enzymes Aldose Reductase and AKR1B10: Structure Determination of Both Ternary Complexes and Implications For Drug Design. Acta Crystallogr.,Sect.D V. 70 889 2014.
ISSN: ISSN 0907-4449
PubMed: 24598757
DOI: 10.1107/S1399004713033452
Page generated: Sun Dec 13 12:04:30 2020

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