Fluorine in PDB 4icc: Crystal Structure of Human AKR1B10 Complexed with Nadp+ and JF0064

The structure of Crystal Structure of Human AKR1B10 Complexed with Nadp+ and JF0064, PDB code: 4icc 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)	23.57 / 1.75
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	79.345, 79.345, 50.174, 90.00, 90.00, 120.00
R / Rfree (%)	16.2 / 18.6

The binding sites of Fluorine atom in the Crystal Structure of Human AKR1B10 Complexed with Nadp+ and JF0064 (pdb code 4icc). 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 AKR1B10 Complexed with Nadp+ and JF0064, PDB code: 4icc:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in the Crystal Structure of Human AKR1B10 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 AKR1B10 Complexed with Nadp+ and JF0064 within 5.0Å range: probe atom residue distance (Å) B Occ X:F402 b:34.6 occ:1.00 F15 X:64I402 0.0 34.6 1.0 C8 X:64I402 1.3 40.9 1.0 C10 X:64I402 2.3 43.3 1.0 C7 X:64I402 2.4 28.5 1.0 F14 X:64I402 2.7 39.6 1.0 CZ2 X:TRP21 2.7 26.0 0.6 C2 X:64I402 2.8 26.9 1.0 F18 X:64I402 2.9 26.8 1.0 C1 X:64I402 3.1 29.1 1.0 NE1 X:TRP21 3.2 23.6 0.4 CZ2 X:TRP21 3.3 30.3 0.4 CE2 X:TRP21 3.3 22.6 0.6 CH2 X:TRP21 3.3 22.4 0.6 CE2 X:TRP21 3.4 25.7 0.4 C9 X:64I402 3.6 25.2 1.0 C12 X:64I402 3.6 40.6 1.0 NE1 X:TRP21 3.7 25.6 0.6 C4 X:64I402 4.0 23.9 1.0 C11 X:64I402 4.1 34.0 1.0 C3 X:64I402 4.3 20.1 1.0 CD2 X:TRP21 4.3 20.1 0.6 CZ3 X:TRP21 4.3 31.2 0.6 CD1 X:TRP21 4.3 20.9 0.4 CH2 X:TRP21 4.4 28.0 0.4 F22 X:64I402 4.5 24.5 1.0 CD2 X:TRP21 4.6 25.5 0.4 F16 X:64I402 4.7 32.4 1.0 O13 X:64I402 4.7 40.1 1.0 CE3 X:TRP21 4.7 25.5 0.6 CD1 X:TRP21 4.8 25.7 0.6 C6 X:64I402 4.9 19.6 1.0

Fluorine binding site 2 out of 8 in the Crystal Structure of Human AKR1B10 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 AKR1B10 Complexed with Nadp+ and JF0064 within 5.0Å range: probe atom residue distance (Å) B Occ X:F402 b:39.6 occ:1.00 F14 X:64I402 0.0 39.6 1.0 C10 X:64I402 1.3 43.3 1.0 C8 X:64I402 2.3 40.9 1.0 C12 X:64I402 2.4 40.6 1.0 F15 X:64I402 2.7 34.6 1.0 O13 X:64I402 2.8 40.1 1.0 C11 X:64I402 3.6 34.0 1.0 C7 X:64I402 3.6 28.5 1.0 CD1 X:TRP220 4.0 58.1 1.0 C9 X:64I402 4.1 25.2 1.0 CZ2 X:TRP21 4.3 26.0 0.6 CH2 X:TRP21 4.3 22.4 0.6 CD X:PRO219 4.4 53.7 1.0 NE1 X:TRP220 4.5 58.8 1.0 F17 X:64I402 4.7 31.5 1.0 C2 X:64I402 4.9 26.9 1.0 CG X:TRP220 4.9 68.5 1.0 F18 X:64I402 4.9 26.8 1.0

Fluorine binding site 3 out of 8 in the Crystal Structure of Human AKR1B10 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 AKR1B10 Complexed with Nadp+ and JF0064 within 5.0Å range: probe atom residue distance (Å) B Occ X:F402 b:31.5 occ:1.00 F17 X:64I402 0.0 31.5 1.0 C11 X:64I402 1.3 34.0 1.0 C12 X:64I402 2.3 40.6 1.0 C9 X:64I402 2.4 25.2 1.0 F16 X:64I402 2.7 32.4 1.0 O13 X:64I402 2.7 40.1 1.0 O X:HOH620 2.8 35.0 1.0 N X:LEU301 2.9 29.6 1.0 N X:ASN300 3.2 23.6 1.0 CA X:CYS299 3.2 24.0 1.0 C X:CYS299 3.3 22.7 1.0 CA X:LEU301 3.5 32.4 1.0 C10 X:64I402 3.6 43.3 1.0 C7 X:64I402 3.6 28.5 1.0 CB X:CYS299 3.7 19.3 1.0 C X:ASN300 3.9 29.2 1.0 CB X:LEU301 3.9 24.7 1.0 CD1 X:LEU301 4.1 37.9 1.0 C8 X:64I402 4.1 40.9 1.0 CA X:ASN300 4.1 30.1 1.0 O X:CYS299 4.1 25.9 1.0 SG X:CYS299 4.4 27.6 1.0 O X:HOH547 4.4 36.4 1.0 O X:ALA298 4.4 24.8 1.0 N X:CYS299 4.5 25.6 1.0 CG X:LEU301 4.7 30.2 1.0 F14 X:64I402 4.7 39.6 1.0 C2 X:64I402 4.9 26.9 1.0 F22 X:64I402 4.9 24.5 1.0 C X:LEU301 4.9 26.0 1.0 C X:ALA298 4.9 25.7 1.0 O X:ASN300 5.0 24.6 1.0 CB X:ASN300 5.0 30.4 1.0

Fluorine binding site 4 out of 8 in the Crystal Structure of Human AKR1B10 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 AKR1B10 Complexed with Nadp+ and JF0064 within 5.0Å range: probe atom residue distance (Å) B Occ X:F402 b:32.4 occ:1.00 F16 X:64I402 0.0 32.4 1.0 C9 X:64I402 1.3 25.2 1.0 C7 X:64I402 2.3 28.5 1.0 C11 X:64I402 2.3 34.0 1.0 F17 X:64I402 2.7 31.5 1.0 F22 X:64I402 2.8 24.5 1.0 C2 X:64I402 2.8 26.9 1.0 C4 X:64I402 2.9 23.9 1.0 CZ2 X:TRP112 3.4 23.1 1.0 CB X:CYS299 3.4 19.3 1.0 C8 X:64I402 3.6 40.9 1.0 C12 X:64I402 3.6 40.6 1.0 SG X:CYS299 3.7 27.6 1.0 C1 X:64I402 3.8 29.1 1.0 CH2 X:TRP112 4.0 15.1 1.0 C6 X:64I402 4.0 19.6 1.0 C10 X:64I402 4.1 43.3 1.0 CA X:CYS299 4.1 24.0 1.0 CD1 X:LEU301 4.2 37.9 1.0 CE2 X:TRP112 4.4 19.2 1.0 C X:CYS299 4.5 22.7 1.0 F18 X:64I402 4.5 26.8 1.0 CB X:LEU301 4.5 24.7 1.0 F15 X:64I402 4.7 34.6 1.0 F21 X:64I402 4.7 23.3 1.0 O X:CYS299 4.7 25.9 1.0 C3 X:64I402 4.7 20.1 1.0 O13 X:64I402 4.7 40.1 1.0 OH X:TYR210 4.7 14.8 1.0 N X:LEU301 4.7 29.6 1.0 C5 X:64I402 4.8 21.4 1.0 CG X:LEU301 4.8 30.2 1.0 NE1 X:TRP112 4.8 21.4 1.0 C4N X:NAP401 4.9 22.1 1.0 CA X:LEU301 5.0 32.4 1.0

Fluorine binding site 5 out of 8 in the Crystal Structure of Human AKR1B10 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 AKR1B10 Complexed with Nadp+ and JF0064 within 5.0Å range: probe atom residue distance (Å) B Occ X:F402 b:24.5 occ:1.00 F22 X:64I402 0.0 24.5 1.0 C4 X:64I402 1.3 23.9 1.0 C6 X:64I402 2.3 19.6 1.0 C2 X:64I402 2.4 26.9 1.0 F21 X:64I402 2.6 23.3 1.0 F16 X:64I402 2.8 32.4 1.0 C7 X:64I402 2.9 28.5 1.0 C9 X:64I402 3.1 25.2 1.0 NE1 X:TRP112 3.5 21.4 1.0 C5 X:64I402 3.6 21.4 1.0 C1 X:64I402 3.7 29.1 1.0 CZ2 X:TRP112 3.7 23.1 1.0 CE2 X:TRP112 3.9 19.2 1.0 C8 X:64I402 4.0 40.9 1.0 CD1 X:LEU301 4.0 37.9 1.0 C3 X:64I402 4.1 20.1 1.0 C11 X:64I402 4.2 34.0 1.0 CH2 X:TRP80 4.3 20.2 1.0 F15 X:64I402 4.5 34.6 1.0 CD2 X:LEU301 4.7 34.2 1.0 CD1 X:TRP112 4.7 17.4 1.0 O20 X:64I402 4.7 19.4 1.0 CZ3 X:TRP80 4.7 20.1 1.0 F18 X:64I402 4.8 26.8 1.0 O7N X:NAP401 4.9 16.9 1.0 CG X:LEU301 4.9 30.2 1.0 CH2 X:TRP112 4.9 15.1 1.0 F17 X:64I402 4.9 31.5 1.0 C10 X:64I402 4.9 43.3 1.0

Fluorine binding site 6 out of 8 in the Crystal Structure of Human AKR1B10 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 AKR1B10 Complexed with Nadp+ and JF0064 within 5.0Å range: probe atom residue distance (Å) B Occ X:F402 b:26.8 occ:1.00 F18 X:64I402 0.0 26.8 1.0 C1 X:64I402 1.3 29.1 1.0 C3 X:64I402 2.3 20.1 1.0 C2 X:64I402 2.4 26.9 1.0 F19 X:64I402 2.7 25.6 1.0 F15 X:64I402 2.9 34.6 1.0 C7 X:64I402 2.9 28.5 1.0 NE1 X:TRP21 2.9 23.6 0.4 CD1 X:TRP21 3.0 20.9 0.4 C8 X:64I402 3.1 40.9 1.0 CD2 X:TRP21 3.2 20.1 0.6 CE2 X:TRP21 3.2 22.6 0.6 CE3 X:TRP21 3.3 25.5 0.6 CZ2 X:TRP21 3.4 26.0 0.6 CZ3 X:TRP21 3.4 31.2 0.6 CH2 X:TRP21 3.5 22.4 0.6 C5N X:NAP401 3.5 16.9 1.0 C5 X:64I402 3.6 21.4 1.0 C4 X:64I402 3.6 23.9 1.0 CE2 X:TRP21 3.7 25.7 0.4 CG X:TRP21 3.8 20.2 0.4 NE1 X:TRP21 3.9 25.6 0.6 CG X:TRP21 3.9 20.0 0.6 C9 X:64I402 4.0 25.2 1.0 C4N X:NAP401 4.0 22.1 1.0 SG X:CYS299 4.1 27.6 1.0 C6 X:64I402 4.1 19.6 1.0 CD2 X:TRP21 4.2 25.5 0.4 C10 X:64I402 4.2 43.3 1.0 CD1 X:TRP21 4.3 25.7 0.6 C6N X:NAP401 4.3 15.5 1.0 CZ2 X:TRP21 4.5 30.3 0.4 F16 X:64I402 4.5 32.4 1.0 O2N X:NAP401 4.5 18.2 1.0 O20 X:64I402 4.7 19.4 1.0 CB X:TRP21 4.8 19.1 0.6 CB X:TRP21 4.8 19.1 0.4 F22 X:64I402 4.8 24.5 1.0 C11 X:64I402 4.9 34.0 1.0 F14 X:64I402 4.9 39.6 1.0

Fluorine binding site 7 out of 8 in the Crystal Structure of Human AKR1B10 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 AKR1B10 Complexed with Nadp+ and JF0064 within 5.0Å range: probe atom residue distance (Å) B Occ X:F402 b:25.6 occ:1.00 F19 X:64I402 0.0 25.6 1.0 C3 X:64I402 1.3 20.1 1.0 C5 X:64I402 2.3 21.4 1.0 C1 X:64I402 2.4 29.1 1.0 F18 X:64I402 2.7 26.8 1.0 O20 X:64I402 2.7 19.4 1.0 C5N X:NAP401 2.9 16.9 1.0 C6N X:NAP401 3.0 15.5 1.0 CG X:TRP21 3.1 20.2 0.4 CG X:TRP21 3.2 20.0 0.6 C4N X:NAP401 3.2 22.1 1.0 CD1 X:TRP21 3.3 20.9 0.4 CB X:TRP21 3.3 19.1 0.4 CB X:TRP21 3.3 19.1 0.6 N1N X:NAP401 3.4 18.6 1.0 OH X:TYR49 3.4 15.3 1.0 CD2 X:TRP21 3.5 20.1 0.6 C3N X:NAP401 3.5 18.0 1.0 C2N X:NAP401 3.6 15.8 1.0 C6 X:64I402 3.6 19.6 1.0 C2 X:64I402 3.6 26.9 1.0 CD1 X:TRP21 3.6 25.7 0.6 CD2 X:TRP21 3.7 25.5 0.4 CE1 X:TYR49 3.9 16.6 1.0 CZ X:TYR49 3.9 16.3 1.0 NE1 X:TRP21 3.9 23.6 0.4 C2D X:NAP401 4.0 18.8 1.0 CE3 X:TRP21 4.0 25.5 0.6 C4 X:64I402 4.1 23.9 1.0 CE2 X:TRP21 4.1 22.6 0.6 CE2 X:TRP21 4.2 25.7 0.4 NE1 X:TRP21 4.2 25.6 0.6 C1D X:NAP401 4.3 17.0 1.0 C3D X:NAP401 4.4 13.2 1.0 CE3 X:TRP21 4.5 22.1 0.4 C7N X:NAP401 4.6 20.8 1.0 F21 X:64I402 4.7 23.3 1.0 CA X:TRP21 4.8 16.2 0.6 CA X:TRP21 4.8 16.2 0.4 O7N X:NAP401 4.9 16.9 1.0 C7 X:64I402 4.9 28.5 1.0 O2N X:NAP401 4.9 18.2 1.0 CZ3 X:TRP21 4.9 31.2 0.6 CD1 X:TYR49 5.0 16.2 1.0 CE2 X:TYR49 5.0 18.0 1.0

Fluorine binding site 8 out of 8 in the Crystal Structure of Human AKR1B10 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 AKR1B10 Complexed with Nadp+ and JF0064 within 5.0Å range: probe atom residue distance (Å) B Occ X:F402 b:23.3 occ:1.00 F21 X:64I402 0.0 23.3 1.0 C6 X:64I402 1.3 19.6 1.0 C4 X:64I402 2.3 23.9 1.0 C5 X:64I402 2.4 21.4 1.0 F22 X:64I402 2.6 24.5 1.0 O20 X:64I402 2.8 19.4 1.0 NE1 X:TRP112 2.8 21.4 1.0 NE2 X:HIS111 2.8 15.3 1.0 CD2 X:HIS111 3.3 14.6 1.0 CZ3 X:TRP80 3.4 20.1 1.0 O7N X:NAP401 3.5 16.9 1.0 CE1 X:HIS111 3.6 15.6 1.0 C3 X:64I402 3.6 20.1 1.0 C2 X:64I402 3.6 26.9 1.0 CD1 X:TRP112 3.7 17.4 1.0 CH2 X:TRP80 3.8 20.2 1.0 CE2 X:TRP112 3.9 19.2 1.0 C1 X:64I402 4.1 29.1 1.0 C7N X:NAP401 4.2 20.8 1.0 CG X:HIS111 4.2 13.9 1.0 CZ2 X:TRP112 4.3 23.1 1.0 ND1 X:HIS111 4.3 14.3 1.0 CE3 X:TRP80 4.5 15.4 1.0 F16 X:64I402 4.7 32.4 1.0 CG1 X:VAL48 4.7 14.9 1.0 F19 X:64I402 4.7 25.6 1.0 C3N X:NAP401 4.8 18.0 1.0 C7 X:64I402 4.9 28.5 1.0 C4N X:NAP401 4.9 22.1 1.0 CG X:TRP112 4.9 19.2 1.0

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