Zinc in PDB 6tw0: Human CD73 (Ecto 5'-Nucleotidase) in Complex with PSB12690 (An Aopcp Derivative, Compound 10 in Publication) in the Closed State

All present enzymatic activity of Human CD73 (Ecto 5'-Nucleotidase) in Complex with PSB12690 (An Aopcp Derivative, Compound 10 in Publication) in the Closed State:
3.1.3.5;

The structure of Human CD73 (Ecto 5'-Nucleotidase) in Complex with PSB12690 (An Aopcp Derivative, Compound 10 in Publication) in the Closed State, PDB code: 6tw0 was solved by J.Pippel, N.Strater, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.12 / 2.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	54.451, 98.343, 233.750, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 26.6

The binding sites of Zinc atom in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with PSB12690 (An Aopcp Derivative, Compound 10 in Publication) in the Closed State (pdb code 6tw0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with PSB12690 (An Aopcp Derivative, Compound 10 in Publication) in the Closed State, PDB code: 6tw0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with PSB12690 (An Aopcp Derivative, Compound 10 in Publication) in the Closed State


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 PSB12690 (An Aopcp Derivative, Compound 10 in Publication) in the Closed State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:63.4 occ:1.00 O A:HOH703 1.9 78.9 1.0 OD1 A:ASP36 2.0 66.6 1.0 NE2 A:HIS38 2.0 62.4 1.0 OD2 A:ASP85 2.4 75.1 1.0 O2B A:NYZ603 2.7 79.8 1.0 O3B A:NYZ603 2.8 83.1 1.0 HB3 A:ASP36 2.9 60.8 1.0 HB3 A:ASP85 2.9 74.9 1.0 CD2 A:HIS38 3.0 62.2 1.0 CE1 A:HIS38 3.0 64.3 1.0 CG A:ASP36 3.0 63.2 1.0 HD2 A:HIS38 3.2 60.1 1.0 CG A:ASP85 3.3 76.6 1.0 HE1 A:HIS38 3.3 65.3 1.0 PB A:NYZ603 3.3 81.6 1.0 CB A:ASP36 3.4 58.5 1.0 CB A:ASP85 3.4 73.8 1.0 HB2 A:ASP85 3.5 72.1 1.0 HA A:ASP36 3.6 58.3 1.0 HD2 A:HIS118 3.6 81.7 1.0 HE1 A:HIS220 3.7 70.7 1.0 ZN A:ZN602 3.8 72.2 1.0 HA A:HIS243 3.9 65.0 1.0 OD1 A:ASN245 4.0 90.0 1.0 CA A:ASP36 4.1 57.4 1.0 CG A:HIS38 4.1 63.9 1.0 ND1 A:HIS38 4.1 66.5 1.0 OD2 A:ASP36 4.1 59.2 1.0 HH22 A:ARG395 4.2 67.4 1.0 HH12 A:ARG395 4.2 84.5 1.0 O1A A:NYZ603 4.3 79.1 1.0 CD2 A:HIS118 4.3 83.7 1.0 HD21 A:ASN245 4.3 98.2 1.0 HB2 A:ASP36 4.3 57.0 1.0 C3A A:NYZ603 4.4 81.0 1.0 H3A1 A:NYZ603 4.4 80.7 1.0 OD1 A:ASP85 4.4 79.1 1.0 O1B A:NYZ603 4.5 83.6 1.0 CE1 A:HIS220 4.5 71.2 1.0 NE2 A:HIS220 4.6 73.8 1.0 H A:HIS243 4.7 61.9 1.0 O A:HIS243 4.8 72.3 1.0 CA A:HIS243 4.9 64.8 1.0 NE2 A:HIS118 4.9 85.4 1.0 PA A:NYZ603 4.9 81.1 1.0 NH2 A:ARG395 4.9 66.0 1.0 CA A:ASP85 4.9 72.5 1.0 NH1 A:ARG395 4.9 82.9 1.0 O A:ASP85 4.9 72.0 1.0 CG A:ASN245 5.0 96.1 1.0

Zinc binding site 2 out of 2 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with PSB12690 (An Aopcp Derivative, Compound 10 in Publication) in the Closed State


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 PSB12690 (An Aopcp Derivative, Compound 10 in Publication) in the Closed State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:72.2 occ:1.00 O3B A:NYZ603 1.9 83.1 1.0 OD1 A:ASN117 2.0 0.8 1.0 NE2 A:HIS220 2.1 73.8 1.0 OD2 A:ASP85 2.3 75.1 1.0 ND1 A:HIS243 2.3 74.5 1.0 HD22 A:ASN117 2.9 99.7 1.0 HA A:HIS243 2.9 65.0 1.0 CG A:ASN117 3.0 0.7 1.0 CD2 A:HIS220 3.0 74.4 1.0 CG A:ASP85 3.1 76.6 1.0 CE1 A:HIS220 3.1 71.2 1.0 CE1 A:HIS243 3.1 77.0 1.0 PB A:NYZ603 3.1 81.6 1.0 HD2 A:HIS118 3.2 81.7 1.0 HE1 A:HIS243 3.2 79.1 1.0 HD2 A:HIS220 3.2 76.2 1.0 HE1 A:HIS220 3.3 70.7 1.0 ND2 A:ASN117 3.4 0.8 1.0 OD1 A:ASP85 3.4 79.1 1.0 CG A:HIS243 3.4 72.1 1.0 O1B A:NYZ603 3.4 83.6 1.0 H A:ASN117 3.5 75.6 1.0 HB2 A:HIS243 3.7 67.0 1.0 CB A:HIS243 3.8 66.7 1.0 ZN A:ZN601 3.8 63.4 1.0 CA A:HIS243 3.8 64.8 1.0 OD1 A:ASP36 3.9 66.6 1.0 H3A1 A:NYZ603 4.0 80.7 1.0 O2B A:NYZ603 4.1 79.8 1.0 H A:HIS118 4.1 75.6 1.0 C3A A:NYZ603 4.2 81.0 1.0 CG A:HIS220 4.2 70.5 1.0 CD2 A:HIS118 4.2 83.7 1.0 ND1 A:HIS220 4.2 70.4 1.0 HB2 A:ASP85 4.3 72.1 1.0 NE2 A:HIS243 4.3 78.3 1.0 CB A:ASP85 4.3 73.8 1.0 HD21 A:ASN117 4.4 0.2 1.0 CB A:ASN117 4.4 83.5 1.0 N A:ASN117 4.4 76.8 1.0 H3A2 A:NYZ603 4.5 81.1 1.0 CD2 A:HIS243 4.5 76.4 1.0 O A:HIS243 4.5 72.3 1.0 HB3 A:ASN117 4.6 83.5 1.0 C A:HIS243 4.7 71.7 1.0 H A:HIS243 4.7 61.9 1.0 HB3 A:ASP85 4.8 74.9 1.0 N A:HIS243 4.8 62.6 1.0 HA3 A:GLY116 4.8 68.6 1.0 HB3 A:HIS243 4.9 66.9 1.0 NE2 A:HIS118 4.9 85.4 1.0 HD13 A:LEU184 4.9 95.2 1.0 CA A:ASN117 4.9 79.9 1.0 N A:HIS118 5.0 78.1 1.0

S.Bhattarai, J.Pippel, E.R.Scaletti, R.Idris, M.Freundlieb, G.Rolshoven, C.Renn, S.Y.Lee, A.Abdelrahman, H.Zimmermann, A.El-Tayeb, C.E.Muller, N.Strater. 2-Substituted Alpha , Beta Methylene-Adp Derivatives: Potent Competitive Ecto-5'-Nucleotidase (CD73) Inhibitors with Variable Binding Modes. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32045236
DOI: 10.1021/ACS.JMEDCHEM.9B01611