Zinc in PDB 6tvx: Human CD73 (Ecto 5'-Nucleotidase) in Complex with PSB12676 (An Aopcp Derivative, Compound 9 in Paper) in the Closed State

All present enzymatic activity of Human CD73 (Ecto 5'-Nucleotidase) in Complex with PSB12676 (An Aopcp Derivative, Compound 9 in Paper) in the Closed State:
3.1.3.5;

The structure of Human CD73 (Ecto 5'-Nucleotidase) in Complex with PSB12676 (An Aopcp Derivative, Compound 9 in Paper) in the Closed State, PDB code: 6tvx 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)	47.70 / 2.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	54.519, 97.453, 233.697, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 24.9

The binding sites of Zinc atom in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with PSB12676 (An Aopcp Derivative, Compound 9 in Paper) in the Closed State (pdb code 6tvx). 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 PSB12676 (An Aopcp Derivative, Compound 9 in Paper) in the Closed State, PDB code: 6tvx:
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 PSB12676 (An Aopcp Derivative, Compound 9 in Paper) 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 PSB12676 (An Aopcp Derivative, Compound 9 in Paper) in the Closed State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:63.1 occ:1.00 O A:HOH701 1.9 0.9 1.0 NE2 A:HIS38 1.9 67.4 1.0 OD2 A:ASP85 2.2 80.5 1.0 O3B A:NYW603 2.2 81.0 1.0 HB3 A:ASP36 2.6 60.9 1.0 CE1 A:HIS38 2.8 69.1 1.0 HE1 A:HIS38 2.9 69.3 1.0 HB3 A:ASP85 2.9 71.4 1.0 OD1 A:ASP36 2.9 73.4 1.0 CD2 A:HIS38 3.1 65.3 1.0 CG A:ASP85 3.2 78.5 1.0 CG A:ASP36 3.3 72.2 1.0 HA A:ASP36 3.3 59.0 1.0 CB A:ASP36 3.3 57.4 1.0 CB A:ASP85 3.4 70.6 1.0 HH12 A:ARG395 3.4 71.0 1.0 HB2 A:ASP85 3.4 69.7 1.0 HD2 A:HIS38 3.5 65.0 1.0 PB A:NYW603 3.5 80.0 1.0 HE1 A:HIS220 3.5 67.5 1.0 ZN A:ZN602 3.8 69.3 1.0 H3A1 A:NYW603 3.9 83.1 1.0 CA A:ASP36 3.9 58.6 1.0 ND1 A:HIS38 4.0 70.5 1.0 O1B A:NYW603 4.0 79.2 1.0 HH22 A:ARG395 4.0 66.4 1.0 CG A:HIS38 4.1 66.9 1.0 C3A A:NYW603 4.2 83.0 1.0 HA A:HIS243 4.2 63.9 1.0 OD1 A:ASN245 4.2 67.1 1.0 OD2 A:ASP36 4.3 75.8 1.0 HB2 A:ASP36 4.3 53.7 1.0 O1A A:NYW603 4.3 82.4 1.0 OD1 A:ASP85 4.3 79.4 1.0 NH1 A:ARG395 4.4 70.8 1.0 CE1 A:HIS220 4.5 67.6 1.0 HD21 A:ASN245 4.6 84.6 1.0 O2B A:NYW603 4.7 80.1 1.0 PA A:NYW603 4.8 83.0 1.0 H A:ASP36 4.8 54.5 1.0 HD1 A:HIS38 4.8 70.6 1.0 CA A:ASP85 4.9 71.6 1.0 N A:ASP36 4.9 54.3 1.0 NH2 A:ARG395 4.9 66.5 1.0 C A:ASP36 4.9 58.1 1.0 NE2 A:HIS220 4.9 70.1 1.0 O A:ASP85 5.0 72.3 1.0 HH11 A:ARG395 5.0 70.7 1.0

Zinc binding site 2 out of 2 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with PSB12676 (An Aopcp Derivative, Compound 9 in Paper) 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 PSB12676 (An Aopcp Derivative, Compound 9 in Paper) in the Closed State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:69.3 occ:1.00 O1B A:NYW603 1.9 79.2 1.0 NE2 A:HIS220 1.9 70.1 1.0 ND1 A:HIS243 2.3 73.5 1.0 OD1 A:ASN117 2.4 93.4 1.0 OD2 A:ASP85 2.5 80.5 1.0 CE1 A:HIS220 2.7 67.6 1.0 HE1 A:HIS220 2.7 67.5 1.0 HA A:HIS243 2.9 63.9 1.0 CE1 A:HIS243 3.0 77.1 1.0 PB A:NYW603 3.0 80.0 1.0 HE1 A:HIS243 3.1 77.5 1.0 O A:HOH701 3.1 0.9 1.0 CG A:ASP85 3.1 78.5 1.0 CD2 A:HIS220 3.2 73.2 1.0 OD1 A:ASP85 3.3 79.4 1.0 CG A:HIS243 3.3 70.7 1.0 O3B A:NYW603 3.4 81.0 1.0 CG A:ASN117 3.4 0.6 1.0 H3A1 A:NYW603 3.5 83.1 1.0 HD22 A:ASN117 3.5 97.0 1.0 HD2 A:HIS220 3.6 73.5 1.0 C3A A:NYW603 3.8 83.0 1.0 HB2 A:HIS243 3.8 65.0 1.0 CA A:HIS243 3.8 63.7 1.0 CB A:HIS243 3.8 65.4 1.0 ZN A:ZN601 3.8 63.1 1.0 H A:ASN117 3.9 76.5 1.0 ND2 A:ASN117 3.9 99.0 1.0 ND1 A:HIS220 3.9 66.6 1.0 H3A2 A:NYW603 4.0 82.9 1.0 CG A:HIS220 4.1 67.5 1.0 NE2 A:HIS243 4.2 76.1 1.0 HB2 A:ASP85 4.3 69.7 1.0 OD1 A:ASP36 4.3 73.4 1.0 CD2 A:HIS243 4.3 74.8 1.0 O2B A:NYW603 4.3 80.1 1.0 CB A:ASP85 4.4 70.6 1.0 H A:HIS118 4.4 78.3 1.0 O A:HIS243 4.4 64.5 1.0 N A:ASN117 4.7 76.7 1.0 N A:HIS243 4.7 59.4 1.0 C A:HIS243 4.7 64.3 1.0 ND1 A:HIS118 4.7 86.0 1.0 CB A:ASN117 4.7 85.6 1.0 HD1 A:HIS220 4.8 66.3 1.0 HB3 A:ASP85 4.8 71.4 1.0 HD21 A:ASN117 4.9 0.2 1.0 HB3 A:ASN117 4.9 84.9 1.0 HB3 A:HIS243 4.9 65.7 1.0 HE1 A:HIS38 4.9 69.3 1.0 CE1 A:HIS118 4.9 85.5 1.0 HA3 A:GLY116 4.9 69.4 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