Fluorine in PDB 5liw: Crystal Structure of Human AKR1B10 Complexed with Nadp+ and the Inhibitor MK319

The structure of Crystal Structure of Human AKR1B10 Complexed with Nadp+ and the Inhibitor MK319, PDB code: 5liw was solved by A.Cousido-Siah, F.X.Ruiz, A.Mitschler, J.Fanfrlik, M.Kamlar, J.Vesely, P.Hobza, A.Podjarny, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.09 / 1.75
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	79.585, 79.585, 49.854, 90.00, 90.00, 120.00
R / Rfree (%)	17.8 / 20.9

The structure of Crystal Structure of Human AKR1B10 Complexed with Nadp+ and the Inhibitor MK319 also contains other interesting chemical elements:

Bromine	(Br)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Human AKR1B10 Complexed with Nadp+ and the Inhibitor MK319 (pdb code 5liw). 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 the Inhibitor MK319, PDB code: 5liw:
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 the Inhibitor MK319


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 the Inhibitor MK319 within 5.0Å range: probe atom residue distance (Å) B Occ X:F402 b:35.8 occ:1.00 F27 X:1WX402 0.0 35.8 1.0 C3 X:1WX402 1.3 32.7 1.0 C5 X:1WX402 2.4 34.9 1.0 C1 X:1WX402 2.4 34.4 1.0 F26 X:1WX402 2.7 35.8 1.0 C7 X:1WX402 2.8 31.5 1.0 O X:HOH548 2.9 40.0 1.0 O16 X:1WX402 3.0 33.9 1.0 CZ3 X:TRP112 3.4 26.4 1.0 CE1 X:PHE312 3.5 35.7 1.0 O X:CYS299 3.5 35.6 1.0 C6 X:1WX402 3.6 32.0 1.0 C2 X:1WX402 3.6 32.9 1.0 N8 X:1WX402 3.7 33.9 1.0 C9 X:1WX402 3.8 33.7 1.0 CH2 X:TRP112 3.8 29.8 1.0 CZ X:PHE312 3.9 33.0 1.0 C X:CYS299 4.1 34.4 1.0 C4 X:1WX402 4.1 30.7 1.0 CE3 X:TRP112 4.2 28.3 1.0 CB X:CYS299 4.3 33.8 1.0 OH X:TYR210 4.5 25.2 1.0 CD1 X:PHE312 4.6 31.9 1.0 N X:ASN300 4.7 35.3 0.9 OD1 X:ASN161 4.7 26.1 1.0 F24 X:1WX402 4.7 34.5 1.0 CA X:CYS299 4.8 33.5 1.0 CZ2 X:TRP112 4.8 30.4 1.0 CA X:ASN300 4.8 37.7 0.9

Fluorine binding site 2 out of 8 in the Crystal Structure of Human AKR1B10 Complexed with Nadp+ and the Inhibitor MK319


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 the Inhibitor MK319 within 5.0Å range: probe atom residue distance (Å) B Occ X:F402 b:34.5 occ:1.00 F24 X:1WX402 0.0 34.5 1.0 C2 X:1WX402 1.3 32.9 1.0 C1 X:1WX402 2.4 34.4 1.0 C4 X:1WX402 2.4 30.7 1.0 F25 X:1WX402 2.8 33.3 1.0 C7 X:1WX402 2.8 31.5 1.0 N8 X:1WX402 2.8 33.9 1.0 F25 X:1WX403 3.3 39.9 1.0 C3 X:1WX402 3.6 32.7 1.0 C6 X:1WX402 3.6 32.0 1.0 CZ3 X:TRP80 3.7 28.1 1.0 BR2 X:1WX403 3.8 36.0 1.0 C9 X:1WX402 3.8 33.7 1.0 CH2 X:TRP80 3.8 31.9 1.0 CD2 X:HIS111 4.0 26.3 1.0 C5 X:1WX402 4.1 34.9 1.0 NE2 X:HIS111 4.2 26.1 1.0 O7N X:NAP401 4.3 26.6 1.0 CE3 X:TRP112 4.4 28.3 1.0 CB X:TRP112 4.4 23.5 1.0 C4 X:1WX403 4.4 35.7 1.0 O20 X:1WX402 4.4 27.4 1.0 O16 X:1WX402 4.5 33.9 1.0 C10 X:1WX402 4.5 32.6 1.0 CD2 X:TRP112 4.7 26.8 1.0 C6 X:1WX403 4.7 37.2 1.0 ND2 X:ASN161 4.7 23.8 1.0 CG X:TRP112 4.7 27.4 1.0 F27 X:1WX402 4.7 35.8 1.0 O X:HIS111 4.9 23.4 1.0 CG X:HIS111 4.9 24.4 1.0 CD1 X:LEU302 4.9 39.6 1.0 O17 X:1WX402 5.0 31.2 1.0 CE3 X:TRP80 5.0 26.1 1.0

Fluorine binding site 3 out of 8 in the Crystal Structure of Human AKR1B10 Complexed with Nadp+ and the Inhibitor MK319


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 the Inhibitor MK319 within 5.0Å range: probe atom residue distance (Å) B Occ X:F402 b:33.3 occ:1.00 F25 X:1WX402 0.0 33.3 1.0 C4 X:1WX402 1.4 30.7 1.0 C6 X:1WX402 2.4 32.0 1.0 C2 X:1WX402 2.4 32.9 1.0 F24 X:1WX402 2.8 34.5 1.0 BR2 X:1WX402 3.0 40.3 1.0 CH2 X:TRP80 3.5 31.9 1.0 CZ X:PHE116 3.6 28.8 1.0 CG X:TRP112 3.6 27.4 1.0 C5 X:1WX402 3.6 34.9 1.0 C1 X:1WX402 3.7 34.4 1.0 F25 X:1WX403 3.7 39.9 1.0 CE2 X:PHE116 3.7 28.0 1.0 CD2 X:TRP112 3.8 26.8 1.0 CD1 X:TRP112 3.9 27.9 1.0 CB X:TRP112 3.9 23.5 1.0 CD1 X:LEU302 4.1 39.6 1.0 CZ3 X:TRP80 4.1 28.1 1.0 C3 X:1WX402 4.1 32.7 1.0 CE2 X:TRP112 4.2 30.8 1.0 NE1 X:TRP112 4.2 29.5 1.0 CZ2 X:TRP80 4.3 27.6 1.0 CE3 X:TRP112 4.3 28.3 1.0 F26 X:1WX402 4.7 35.8 1.0 C7 X:1WX402 4.9 31.5 1.0 CE1 X:PHE116 4.9 27.1 1.0 C4 X:1WX403 4.9 35.7 1.0 O X:HOH634 4.9 35.8 0.7

Fluorine binding site 4 out of 8 in the Crystal Structure of Human AKR1B10 Complexed with Nadp+ and the Inhibitor MK319


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 the Inhibitor MK319 within 5.0Å range: probe atom residue distance (Å) B Occ X:F402 b:35.8 occ:1.00 F26 X:1WX402 0.0 35.8 1.0 C5 X:1WX402 1.4 34.9 1.0 C6 X:1WX402 2.4 32.0 1.0 C3 X:1WX402 2.4 32.7 1.0 F27 X:1WX402 2.7 35.8 1.0 O X:HOH548 3.0 40.0 1.0 BR2 X:1WX402 3.1 40.3 1.0 CH2 X:TRP112 3.1 29.8 1.0 CZ2 X:TRP112 3.4 30.4 1.0 CB X:LEU302 3.6 41.2 1.0 C4 X:1WX402 3.6 30.7 1.0 C1 X:1WX402 3.6 34.4 1.0 CZ3 X:TRP112 3.7 26.4 1.0 C2 X:1WX402 4.1 32.9 1.0 CE2 X:TRP112 4.2 30.8 1.0 O X:LEU302 4.3 47.3 1.0 OG X:SER304 4.3 42.9 1.0 CG X:LEU302 4.4 42.4 1.0 CD1 X:LEU302 4.4 39.6 1.0 CE3 X:TRP112 4.4 28.3 1.0 CA X:LEU302 4.4 43.7 1.0 CE1 X:PHE312 4.5 35.7 1.0 N X:LEU302 4.5 41.2 1.0 C X:LEU302 4.6 47.2 1.0 CD2 X:TRP112 4.6 26.8 1.0 O16 X:1WX402 4.6 33.9 1.0 F25 X:1WX402 4.7 33.3 1.0 CE1 X:TYR310 4.8 31.3 1.0 C7 X:1WX402 4.9 31.5 1.0 OH X:TYR310 4.9 35.1 1.0 CD1 X:PHE312 5.0 31.9 1.0

Fluorine binding site 5 out of 8 in the Crystal Structure of Human AKR1B10 Complexed with Nadp+ and the Inhibitor MK319


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 the Inhibitor MK319 within 5.0Å range: probe atom residue distance (Å) B Occ X:F403 b:43.9 occ:1.00 F27 X:1WX403 0.0 43.9 1.0 C3 X:1WX403 1.3 40.0 1.0 C5 X:1WX403 2.3 39.0 1.0 C1 X:1WX403 2.4 36.5 1.0 F26 X:1WX403 2.7 38.3 1.0 O20 X:1WX403 2.8 40.6 1.0 C7 X:1WX403 2.8 41.5 1.0 N8 X:1WX403 3.2 43.9 1.0 O X:HOH631 3.4 40.8 1.0 CZ X:PHE123 3.5 34.5 1.0 CL2 X:1WX402 3.5 33.8 1.0 C6 X:1WX403 3.6 37.2 1.0 C2 X:1WX403 3.6 41.8 1.0 O X:HOH528 3.9 28.9 1.0 CE1 X:PHE123 3.9 35.2 1.0 C19 X:1WX403 4.0 44.9 1.0 C4 X:1WX403 4.1 35.7 1.0 CE2 X:PHE123 4.2 36.2 1.0 C15 X:1WX402 4.4 34.3 1.0 O17 X:1WX403 4.4 41.3 1.0 C9 X:1WX403 4.5 45.5 1.0 F24 X:1WX403 4.7 45.0 1.0 CG2 X:VAL48 4.8 29.3 1.0 C18 X:1WX403 4.8 40.2 1.0 CD1 X:PHE123 4.9 32.9 1.0 O21 X:1WX403 4.9 45.5 1.0 C13 X:1WX402 4.9 32.8 1.0 O X:VAL48 5.0 28.4 1.0

Fluorine binding site 6 out of 8 in the Crystal Structure of Human AKR1B10 Complexed with Nadp+ and the Inhibitor MK319


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 the Inhibitor MK319 within 5.0Å range: probe atom residue distance (Å) B Occ X:F403 b:45.0 occ:1.00 F24 X:1WX403 0.0 45.0 1.0 C2 X:1WX403 1.3 41.8 1.0 C4 X:1WX403 2.4 35.7 1.0 C1 X:1WX403 2.4 36.5 1.0 F25 X:1WX403 2.7 39.9 1.0 NH2 X:ARG125 2.8 41.2 0.5 NH2 X:ARG125 2.8 41.2 0.5 C7 X:1WX403 2.8 41.5 1.0 O16 X:1WX403 3.1 46.9 1.0 CD1 X:LEU302 3.2 39.6 1.0 N8 X:1WX403 3.6 43.9 1.0 C6 X:1WX403 3.6 37.2 1.0 C3 X:1WX403 3.6 40.0 1.0 CD1 X:PHE123 3.7 32.9 1.0 C9 X:1WX403 3.7 45.5 1.0 CD2 X:LEU302 3.9 47.3 1.0 CE1 X:PHE123 4.0 35.2 1.0 O X:HOH634 4.0 35.8 0.7 CZ X:ARG125 4.1 42.3 0.5 CZ X:ARG125 4.1 42.3 0.5 C14 X:1WX402 4.1 35.0 1.0 CG X:LEU302 4.1 42.4 1.0 C5 X:1WX403 4.1 39.0 1.0 C12 X:1WX402 4.3 36.6 1.0 CG X:PHE123 4.6 34.4 1.0 CH2 X:TRP80 4.7 31.9 1.0 F27 X:1WX403 4.7 43.9 1.0 CZ2 X:TRP80 4.8 27.6 1.0 C15 X:1WX402 4.8 34.3 1.0 NE X:ARG125 4.8 40.9 0.5 NE X:ARG125 4.8 40.9 0.5 NH1 X:ARG125 4.9 42.9 0.5 NH1 X:ARG125 4.9 42.9 0.5 CZ X:PHE123 5.0 34.5 1.0

Fluorine binding site 7 out of 8 in the Crystal Structure of Human AKR1B10 Complexed with Nadp+ and the Inhibitor MK319


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 the Inhibitor MK319 within 5.0Å range: probe atom residue distance (Å) B Occ X:F403 b:39.9 occ:1.00 F25 X:1WX403 0.0 39.9 1.0 C4 X:1WX403 1.3 35.7 1.0 C2 X:1WX403 2.4 41.8 1.0 C6 X:1WX403 2.4 37.2 1.0 F24 X:1WX403 2.7 45.0 1.0 BR2 X:1WX403 3.0 36.0 1.0 CD1 X:LEU302 3.1 39.6 1.0 F24 X:1WX402 3.3 34.5 1.0 CH2 X:TRP80 3.3 31.9 1.0 C12 X:1WX402 3.3 36.6 1.0 C10 X:1WX402 3.5 32.6 1.0 C2 X:1WX402 3.6 32.9 1.0 C1 X:1WX403 3.6 36.5 1.0 C5 X:1WX403 3.6 39.0 1.0 F25 X:1WX402 3.7 33.3 1.0 C4 X:1WX402 3.7 30.7 1.0 C14 X:1WX402 3.8 35.0 1.0 C9 X:1WX402 3.9 33.7 1.0 N8 X:1WX402 4.0 33.9 1.0 C11 X:1WX402 4.1 34.5 1.0 C3 X:1WX403 4.1 40.0 1.0 CZ3 X:TRP80 4.1 28.1 1.0 CZ2 X:TRP80 4.2 27.6 1.0 C15 X:1WX402 4.3 34.3 1.0 C1 X:1WX402 4.3 34.4 1.0 C13 X:1WX402 4.4 32.8 1.0 CG X:LEU302 4.5 42.4 1.0 C6 X:1WX402 4.6 32.0 1.0 O16 X:1WX402 4.6 33.9 1.0 F26 X:1WX403 4.7 38.3 1.0 C7 X:1WX403 4.9 41.5 1.0 O17 X:1WX402 4.9 31.2 1.0 C7 X:1WX402 4.9 31.5 1.0

Fluorine binding site 8 out of 8 in the Crystal Structure of Human AKR1B10 Complexed with Nadp+ and the Inhibitor MK319


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 the Inhibitor MK319 within 5.0Å range: probe atom residue distance (Å) B Occ X:F403 b:38.3 occ:1.00 F26 X:1WX403 0.0 38.3 1.0 C5 X:1WX403 1.4 39.0 1.0 C6 X:1WX403 2.4 37.2 1.0 O X:HOH631 2.4 40.8 1.0 C3 X:1WX403 2.4 40.0 1.0 F27 X:1WX403 2.7 43.9 1.0 BR2 X:1WX403 3.0 36.0 1.0 C4 X:1WX403 3.6 35.7 1.0 C1 X:1WX403 3.7 36.5 1.0 CG2 X:VAL48 3.7 29.3 1.0 CG1 X:VAL48 3.8 25.2 1.0 C13 X:1WX402 3.9 32.8 1.0 NE1 X:TRP21 3.9 33.0 1.0 O X:VAL48 4.0 28.4 1.0 C2 X:1WX403 4.1 41.8 1.0 C15 X:1WX402 4.2 34.3 1.0 CL2 X:1WX402 4.2 33.8 1.0 CD1 X:TRP21 4.2 30.1 1.0 CB X:VAL48 4.3 28.7 1.0 CD1 X:TYR49 4.5 23.3 1.0 C X:VAL48 4.5 29.9 1.0 O X:HOH528 4.6 28.9 1.0 C11 X:1WX402 4.6 34.5 1.0 F25 X:1WX403 4.7 39.9 1.0 CZ X:PHE123 4.7 34.5 1.0 C18 X:1WX402 4.7 27.3 1.0 CE1 X:PHE123 4.7 35.2 1.0 CE1 X:TYR49 4.8 24.3 1.0 C7 X:1WX403 4.9 41.5 1.0 CE2 X:TRP21 4.9 28.8 1.0 O17 X:1WX402 5.0 31.2 1.0

A.Cousido-Siah, F.X.Ruiz, J.Fanfrlik, J.Gimenez-Dejoz, A.Mitschler, M.Kamlar, J.Vesely, H.Ajani, X.Pares, J.Farres, P.Hobza, A.D.Podjarny. IDD388 Polyhalogenated Derivatives As Probes For An Improved Structure-Based Selectivity of AKR1B10 Inhibitors. Acs Chem.Biol. V. 11 2693 2016.
ISSN: ESSN 1554-8937
PubMed: 27359042
DOI: 10.1021/ACSCHEMBIO.6B00382