Fluorine in PDB 5h08: Human Ptprz D1 Domain Complexed with NAZ2329

All present enzymatic activity of Human Ptprz D1 Domain Complexed with NAZ2329:
3.1.3.48;

The structure of Human Ptprz D1 Domain Complexed with NAZ2329, PDB code: 5h08 was solved by H.Sugawara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.40 / 2.53
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.776, 72.306, 90.796, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 29.7

The binding sites of Fluorine atom in the Human Ptprz D1 Domain Complexed with NAZ2329 (pdb code 5h08). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Human Ptprz D1 Domain Complexed with NAZ2329, PDB code: 5h08:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Human Ptprz D1 Domain Complexed with NAZ2329


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Ptprz D1 Domain Complexed with NAZ2329 within 5.0Å range: probe atom residue distance (Å) B Occ A:F2101 b:35.9 occ:1.00 F3 A:7WL2101 0.0 35.9 1.0 C8 A:7WL2101 1.3 36.7 1.0 F1 A:7WL2101 2.2 36.6 1.0 F2 A:7WL2101 2.2 37.3 1.0 C1 A:7WL2101 2.3 38.0 1.0 C6 A:7WL2101 2.8 38.9 1.0 C2 A:7WL2101 3.6 38.1 1.0 CG2 A:ILE1826 3.6 29.0 1.0 CD1 A:TYR1943 3.7 25.1 1.0 CB A:TYR1943 3.9 22.9 1.0 CD1 A:ILE1826 3.9 26.8 1.0 CG1 A:ILE1826 3.9 27.3 1.0 C5 A:7WL2101 4.1 39.8 1.0 CE2 A:PHE1914 4.2 36.2 1.0 CG A:TYR1943 4.2 23.4 1.0 CD2 A:PHE1914 4.2 37.7 1.0 CB A:ILE1826 4.5 27.5 1.0 CA A:TYR1943 4.6 23.5 1.0 CG2 A:VAL1915 4.6 36.0 1.0 CE1 A:TYR1943 4.7 25.7 1.0 C3 A:7WL2101 4.7 39.0 1.0 C4 A:7WL2101 4.9 40.1 1.0 O A:ARG1939 5.0 22.2 1.0

Fluorine binding site 2 out of 3 in the Human Ptprz D1 Domain Complexed with NAZ2329


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Ptprz D1 Domain Complexed with NAZ2329 within 5.0Å range: probe atom residue distance (Å) B Occ A:F2101 b:36.6 occ:1.00 F1 A:7WL2101 0.0 36.6 1.0 C8 A:7WL2101 1.3 36.7 1.0 F3 A:7WL2101 2.2 35.9 1.0 F2 A:7WL2101 2.2 37.3 1.0 C1 A:7WL2101 2.3 38.0 1.0 C2 A:7WL2101 2.7 38.1 1.0 CB A:TYR1943 3.4 22.9 1.0 N A:TYR1943 3.4 23.3 1.0 CA A:TYR1943 3.5 23.5 1.0 O A:ARG1939 3.5 22.2 1.0 C6 A:7WL2101 3.5 38.9 1.0 C A:THR1942 3.9 24.1 1.0 C3 A:7WL2101 4.0 39.0 1.0 CG2 A:THR1942 4.1 26.1 1.0 CB A:THR1942 4.1 24.3 1.0 CG2 A:ILE1826 4.2 29.0 1.0 CD1 A:ILE1826 4.3 26.8 1.0 CG A:TYR1943 4.4 23.4 1.0 CD1 A:TYR1943 4.4 25.1 1.0 CD1 A:LEU1946 4.4 31.8 1.0 C A:ARG1939 4.5 21.3 1.0 O A:THR1942 4.5 25.2 1.0 CA A:THR1942 4.6 23.7 1.0 C5 A:7WL2101 4.6 39.8 1.0 C4 A:7WL2101 4.8 40.1 1.0 CA A:ARG1939 4.9 22.5 1.0 C9 A:7WL2101 4.9 39.7 1.0 CG1 A:ILE1826 4.9 27.3 1.0 C A:TYR1943 5.0 23.3 1.0

Fluorine binding site 3 out of 3 in the Human Ptprz D1 Domain Complexed with NAZ2329


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Ptprz D1 Domain Complexed with NAZ2329 within 5.0Å range: probe atom residue distance (Å) B Occ A:F2101 b:37.3 occ:1.00 F2 A:7WL2101 0.0 37.3 1.0 C8 A:7WL2101 1.3 36.7 1.0 F3 A:7WL2101 2.2 35.9 1.0 F1 A:7WL2101 2.2 36.6 1.0 C1 A:7WL2101 2.3 38.0 1.0 C2 A:7WL2101 3.2 38.1 1.0 C6 A:7WL2101 3.2 38.9 1.0 CD1 A:LEU1946 3.6 31.8 1.0 CG2 A:VAL1915 3.6 36.0 1.0 CG1 A:VAL1911 3.8 44.3 1.0 CD1 A:TYR1943 4.2 25.1 1.0 CA A:TYR1943 4.3 23.5 1.0 CB A:TYR1943 4.3 22.9 1.0 C5 A:7WL2101 4.4 39.8 1.0 C3 A:7WL2101 4.4 39.0 1.0 N A:TYR1943 4.7 23.3 1.0 CG A:TYR1943 4.8 23.4 1.0 CG A:LEU1946 4.9 32.2 1.0 O A:VAL1911 4.9 44.6 1.0 C4 A:7WL2101 4.9 40.1 1.0

A.Fujikawa, H.Sugawara, T.Tanaka, M.Matsumoto, K.Kuboyama, R.Suzuki, N.Tanga, A.Ogata, M.Masumura, M.Noda. Targeting Ptprz Inhibits Stem Cell-Like Properties and Tumorigenicity in Glioblastoma Cells Sci Rep V. 7 5609 2017.
ISSN: ESSN 2045-2322
PubMed: 28717188
DOI: 10.1038/S41598-017-05931-8