Zinc in PDB 7jv9: Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 12

All present enzymatic activity of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 12:
3.1.3.5;

The structure of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 12, PDB code: 7jv9 was solved by P.Gibbons, X.Du, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	115.97 / 2.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	231.933, 93.794, 54.922, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 27.9

The structure of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 12 also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Zinc atom in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 12 (pdb code 7jv9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 12, PDB code: 7jv9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:0.8 occ:1.00 NE2 A:HIS38 2.1 59.1 1.0 OD1 A:ASP36 2.1 81.5 1.0 OD2 A:ASP85 2.1 60.2 1.0 CE1 A:HIS38 2.3 66.5 1.0 CG A:ASP85 2.9 45.2 1.0 CB A:ASP85 3.1 40.5 1.0 CG A:ASP36 3.3 43.6 1.0 O28 A:VPG605 3.3 54.2 1.0 CD2 A:HIS38 3.4 48.3 1.0 O29 A:VPG605 3.4 53.6 1.0 ND1 A:HIS38 3.5 55.8 1.0 ZN A:ZN602 3.6 47.1 1.0 P26 A:VPG605 3.7 51.6 1.0 O27 A:VPG605 3.8 52.7 1.0 CB A:ASP36 3.9 46.8 1.0 CD2 A:HIS118 4.0 50.5 1.0 CG A:HIS38 4.1 50.7 1.0 OD1 A:ASP85 4.1 45.5 1.0 OD2 A:ASP36 4.3 39.4 1.0 CA A:ASP36 4.3 52.0 1.0 OD1 A:ASN245 4.3 50.8 1.0 NE2 A:HIS118 4.5 50.4 1.0 CE1 A:HIS220 4.5 32.5 1.0 NH1 A:ARG395 4.5 61.9 1.0 CA A:ASP85 4.6 40.3 1.0 NE2 A:HIS220 4.7 42.5 1.0 O A:HIS243 4.8 81.9 1.0 O A:ASP85 4.8 46.7 1.0 CG A:HIS118 5.0 48.5 1.0

Zinc binding site 2 out of 4 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:47.1 occ:1.00 O29 A:VPG605 2.0 53.6 1.0 OD1 A:ASN117 2.1 38.3 1.0 ND1 A:HIS243 2.1 52.8 1.0 OD2 A:ASP85 2.1 60.2 1.0 NE2 A:HIS220 2.1 42.5 1.0 CE1 A:HIS243 2.9 52.4 1.0 CG A:ASP85 3.0 45.2 1.0 CE1 A:HIS220 3.0 32.5 1.0 CD2 A:HIS220 3.2 35.8 1.0 CG A:HIS243 3.2 52.4 1.0 CG A:ASN117 3.2 41.3 1.0 OD1 A:ASP85 3.3 45.5 1.0 P26 A:VPG605 3.3 51.6 1.0 ZN A:ZN601 3.6 0.8 1.0 CA A:HIS243 3.6 50.9 1.0 O28 A:VPG605 3.7 54.2 1.0 CB A:HIS243 3.7 51.8 1.0 ND2 A:ASN117 3.8 46.1 1.0 OD1 A:ASP36 3.9 81.5 1.0 O A:HIS243 4.1 81.9 1.0 NE2 A:HIS243 4.1 53.2 1.0 ND1 A:HIS220 4.2 36.0 1.0 CG A:HIS220 4.3 32.9 1.0 CD2 A:HIS243 4.3 54.4 1.0 C25 A:VPG605 4.3 60.1 1.0 CB A:ASP85 4.3 40.5 1.0 CD2 A:HIS118 4.3 50.5 1.0 O27 A:VPG605 4.4 52.7 1.0 C A:HIS243 4.4 62.5 1.0 CB A:ASN117 4.5 43.1 1.0 N A:HIS243 4.7 36.5 1.0 N A:ASN117 4.7 37.9 1.0 CG A:ASP36 4.9 43.6 1.0

Zinc binding site 3 out of 4 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 12 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:74.3 occ:1.00 O28 B:VPG605 2.1 94.4 1.0 OD1 B:ASP36 2.1 55.1 1.0 NE2 B:HIS38 2.1 55.2 1.0 OD2 B:ASP85 2.1 47.2 1.0 CE1 B:HIS38 2.4 45.6 1.0 CG B:ASP85 3.0 37.2 1.0 CB B:ASP85 3.1 37.5 1.0 CG B:ASP36 3.3 41.8 1.0 P26 B:VPG605 3.4 59.0 1.0 CD2 B:HIS38 3.4 47.3 1.0 ZN B:ZN602 3.6 42.8 1.0 ND1 B:HIS38 3.6 41.6 1.0 O29 B:VPG605 3.6 56.3 1.0 CB B:ASP36 3.9 42.4 1.0 CD2 B:HIS118 3.9 50.9 1.0 O27 B:VPG605 4.0 58.6 1.0 CG B:HIS38 4.1 46.9 1.0 OD1 B:ASP85 4.1 42.0 1.0 OD2 B:ASP36 4.3 39.5 1.0 CA B:ASP36 4.3 37.7 1.0 OD1 B:ASN245 4.4 51.1 1.0 NE2 B:HIS118 4.4 50.5 1.0 NH1 B:ARG395 4.4 65.4 1.0 CE1 B:HIS220 4.6 35.1 1.0 CA B:ASP85 4.6 35.2 1.0 NE2 B:HIS220 4.7 41.3 1.0 O B:HIS243 4.8 68.4 1.0 C25 B:VPG605 4.8 67.8 1.0 O B:ASP85 4.8 27.0 1.0 CG B:HIS118 4.9 48.6 1.0

Zinc binding site 4 out of 4 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 12 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:42.8 occ:1.00 O29 B:VPG605 2.0 56.3 1.0 OD1 B:ASN117 2.1 38.0 1.0 OD2 B:ASP85 2.1 47.2 1.0 ND1 B:HIS243 2.1 58.6 1.0 NE2 B:HIS220 2.1 41.3 1.0 CE1 B:HIS243 3.0 60.3 1.0 CG B:ASP85 3.0 37.2 1.0 CE1 B:HIS220 3.0 35.1 1.0 P26 B:VPG605 3.2 59.0 1.0 CD2 B:HIS220 3.2 36.4 1.0 CG B:ASN117 3.2 40.9 1.0 CG B:HIS243 3.2 57.8 1.0 OD1 B:ASP85 3.3 42.0 1.0 O28 B:VPG605 3.4 94.4 1.0 ZN B:ZN601 3.6 74.3 1.0 CA B:HIS243 3.6 53.5 1.0 CB B:HIS243 3.7 55.0 1.0 ND2 B:ASN117 3.8 42.2 1.0 OD1 B:ASP36 3.9 55.1 1.0 C25 B:VPG605 4.1 67.8 1.0 O B:HIS243 4.1 68.4 1.0 NE2 B:HIS243 4.1 63.6 1.0 ND1 B:HIS220 4.2 35.5 1.0 CD2 B:HIS118 4.2 50.9 1.0 CG B:HIS220 4.3 34.0 1.0 CB B:ASP85 4.3 37.5 1.0 CD2 B:HIS243 4.3 54.4 1.0 C B:HIS243 4.4 61.2 1.0 O27 B:VPG605 4.4 58.6 1.0 CB B:ASN117 4.5 42.0 1.0 N B:ASN117 4.7 37.2 1.0 N B:HIS243 4.7 48.0 1.0 NE2 B:HIS118 4.9 50.5 1.0 CG B:ASP36 4.9 41.8 1.0

X.Du, J.Moore, B.R.Blank, J.Eksterowicz, D.Sutimantanapi, N.Yuen, T.Metzger, B.Chan, T.Huang, X.Chen, Y.Chen, F.Duong, W.Kong, J.H.Chang, J.Sun, T.Zavorotinskaya, Q.Ye, M.R.Junttila, C.Ndubaku, L.S.Friedman, V.R.Fantin, D.Sun. Orally Bioavailable Small-Molecule CD73 Inhibitor (Op-5244) Reverses Immunosuppression Through Blockade of Adenosine Production. J.Med.Chem. V. 63 10433 2020.
ISSN: ISSN 0022-2623
PubMed: 32865411
DOI: 10.1021/ACS.JMEDCHEM.0C01086