Fluorine in PDB 4gm8: Crystal Structure of Human Wd Repeat Domain 5 with Compound Mm-102

The structure of Crystal Structure of Human Wd Repeat Domain 5 with Compound Mm-102, PDB code: 4gm8 was solved by H.Karatas, E.C.Townsend, Y.Chen, D.Bernard, F.Cao, L.Liu, M.Lei, Y.Dou, S.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.86 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.861, 106.478, 120.719, 90.00, 90.35, 90.00
R / Rfree (%)	19.3 / 24.9

The binding sites of Fluorine atom in the Crystal Structure of Human Wd Repeat Domain 5 with Compound Mm-102 (pdb code 4gm8). 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 Wd Repeat Domain 5 with Compound Mm-102, PDB code: 4gm8:
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 Wd Repeat Domain 5 with Compound Mm-102


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 Wd Repeat Domain 5 with Compound Mm-102 within 5.0Å range: probe atom residue distance (Å) B Occ E:F5 b:69.8 occ:1.00 F01 E:0XN5 0.0 69.8 1.0 CBK E:0XN5 1.3 49.8 1.0 CBJ E:0XN5 2.3 40.3 1.0 CBL E:0XN5 2.4 37.4 1.0 CBI E:0XN5 3.6 48.2 1.0 CBM E:0XN5 3.7 37.8 1.0 O A:LYS259 4.0 29.7 1.0 CBH E:0XN5 4.1 26.4 1.0 C A:LYS259 4.6 18.0 1.0 O A:HOH440 4.6 23.0 1.0 CB A:LYS259 4.7 26.7 1.0 CA A:LYS259 4.8 23.2 1.0

Fluorine binding site 2 out of 8 in the Crystal Structure of Human Wd Repeat Domain 5 with Compound Mm-102


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 Wd Repeat Domain 5 with Compound Mm-102 within 5.0Å range: probe atom residue distance (Å) B Occ E:F5 b:56.4 occ:1.00 F02 E:0XN5 0.0 56.4 1.0 CBP E:0XN5 1.3 28.8 1.0 CBQ E:0XN5 2.3 38.5 1.0 CBO E:0XN5 2.4 27.4 1.0 CBR E:0XN5 3.6 34.9 1.0 CBN E:0XN5 3.7 26.5 1.0 CBG E:0XN5 4.1 24.1 1.0 CBE E:0XL2 4.3 27.6 1.0 CAZ E:0XL2 4.7 22.2 1.0

Fluorine binding site 3 out of 8 in the Crystal Structure of Human Wd Repeat Domain 5 with Compound Mm-102


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 Wd Repeat Domain 5 with Compound Mm-102 within 5.0Å range: probe atom residue distance (Å) B Occ F:F5 b:87.0 occ:1.00 F01 F:0XN5 0.0 87.0 1.0 CBK F:0XN5 1.3 40.7 1.0 CBJ F:0XN5 2.4 41.2 1.0 CBL F:0XN5 2.4 28.9 1.0 O B:HOH473 2.5 32.7 1.0 O B:LYS259 3.5 32.1 1.0 CBI F:0XN5 3.6 47.2 1.0 CBM F:0XN5 3.6 31.9 1.0 CBH F:0XN5 4.1 36.4 1.0 C B:LYS259 4.1 19.5 1.0 CB B:LYS259 4.3 30.7 1.0 CA B:LYS259 4.3 27.6 1.0 OH B:TYR191 4.9 46.4 1.0 CG B:LYS259 4.9 54.7 1.0

Fluorine binding site 4 out of 8 in the Crystal Structure of Human Wd Repeat Domain 5 with Compound Mm-102


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 Wd Repeat Domain 5 with Compound Mm-102 within 5.0Å range: probe atom residue distance (Å) B Occ F:F5 b:63.7 occ:1.00 F02 F:0XN5 0.0 63.7 1.0 CBP F:0XN5 1.3 34.4 1.0 CBO F:0XN5 2.3 40.9 1.0 CBQ F:0XN5 2.4 38.0 1.0 CBN F:0XN5 3.6 43.6 1.0 CBR F:0XN5 3.6 36.3 1.0 CBG F:0XN5 4.1 43.1 1.0 CBE F:0XL2 4.8 27.6 1.0 CAZ F:0XL2 4.8 13.2 1.0

Fluorine binding site 5 out of 8 in the Crystal Structure of Human Wd Repeat Domain 5 with Compound Mm-102


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 Wd Repeat Domain 5 with Compound Mm-102 within 5.0Å range: probe atom residue distance (Å) B Occ G:F5 b:53.7 occ:1.00 F01 G:0XN5 0.0 53.7 1.0 CBK G:0XN5 1.3 33.6 1.0 CBJ G:0XN5 2.4 47.4 1.0 CBL G:0XN5 2.4 40.4 1.0 CBM G:0XN5 3.6 37.7 1.0 CBI G:0XN5 3.6 38.3 1.0 O C:LYS259 3.8 38.1 1.0 CBH G:0XN5 4.1 31.2 1.0 C C:LYS259 4.5 23.3 1.0 CB C:LYS259 4.5 31.7 1.0 CA C:LYS259 4.7 26.4 1.0

Fluorine binding site 6 out of 8 in the Crystal Structure of Human Wd Repeat Domain 5 with Compound Mm-102


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 Wd Repeat Domain 5 with Compound Mm-102 within 5.0Å range: probe atom residue distance (Å) B Occ G:F5 b:53.9 occ:1.00 F02 G:0XN5 0.0 53.9 1.0 CBP G:0XN5 1.3 39.0 1.0 CBQ G:0XN5 2.3 41.2 1.0 CBO G:0XN5 2.4 33.5 1.0 CBR G:0XN5 3.6 36.6 1.0 CBN G:0XN5 3.7 30.4 1.0 CBG G:0XN5 4.1 29.6 1.0 CBE G:0XL2 4.7 22.3 1.0 CAZ G:0XL2 5.0 20.1 1.0

Fluorine binding site 7 out of 8 in the Crystal Structure of Human Wd Repeat Domain 5 with Compound Mm-102


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 Wd Repeat Domain 5 with Compound Mm-102 within 5.0Å range: probe atom residue distance (Å) B Occ H:F5 b:0.8 occ:1.00 F01 H:0XN5 0.0 0.8 1.0 CBK H:0XN5 1.3 53.6 1.0 CBJ H:0XN5 2.4 44.5 1.0 CBL H:0XN5 2.4 47.0 1.0 O D:LYS259 3.3 32.9 1.0 CBI H:0XN5 3.6 38.5 1.0 CBM H:0XN5 3.6 47.2 1.0 C D:LYS259 4.1 21.7 1.0 CBH H:0XN5 4.1 31.9 1.0 CA D:LYS259 4.4 26.2 1.0 CB D:LYS259 4.4 28.5 1.0 OH D:TYR191 4.5 47.7 1.0 O H:HOH101 5.0 16.2 1.0

Fluorine binding site 8 out of 8 in the Crystal Structure of Human Wd Repeat Domain 5 with Compound Mm-102


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 Wd Repeat Domain 5 with Compound Mm-102 within 5.0Å range: probe atom residue distance (Å) B Occ H:F5 b:72.0 occ:1.00 F02 H:0XN5 0.0 72.0 1.0 CBP H:0XN5 1.3 32.4 1.0 CBQ H:0XN5 2.3 46.2 1.0 CBO H:0XN5 2.4 38.1 1.0 CBR H:0XN5 3.6 36.1 1.0 CBN H:0XN5 3.6 32.8 1.0 CBG H:0XN5 4.1 29.2 1.0 CBE H:0XL2 4.7 32.4 1.0 CAZ H:0XL2 4.9 15.3 1.0

H.Karatas, E.C.Townsend, F.Cao, Y.Chen, D.Bernard, L.Liu, M.Lei, Y.Dou, S.Wang. High-Affinity, Small-Molecule Peptidomimetic Inhibitors of MLL1/WDR5 Protein-Protein Interaction. J.Am.Chem.Soc. V. 135 669 2013.
ISSN: ISSN 0002-7863
PubMed: 23210835
DOI: 10.1021/JA306028Q