Zinc in PDB 7jv8: Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35

Enzymatic activity of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35

All present enzymatic activity of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35:
3.1.3.5;

Protein crystallography data

The structure of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35, PDB code: 7jv8 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) 126.17 / 2.46
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.876, 102.354, 129.609, 90.00, 103.22, 90.00
R / Rfree (%) 22 / 27.9

Other elements in 7jv8:

The structure of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35 also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35 (pdb code 7jv8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35, PDB code: 7jv8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7jv8

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Zinc binding site 1 out of 8 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35


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 35 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:34.6
occ:1.00
 OD2 A:ASP36 2.0 29.3 1.0
OD2 A:ASP85 2.1 33.5 1.0
O A:HOH720 2.1 22.4 1.0
NE2 A:HIS38 2.2 34.0 1.0
O1 A:VPD604 2.2 30.2 1.0
O4 A:VPD604 2.9 23.0 1.0
CG A:ASP85 3.0 26.1 1.0
P2 A:VPD604 3.1 28.6 1.0
CE1 A:HIS38 3.1 29.1 1.0
CG A:ASP36 3.1 30.1 1.0
CD2 A:HIS38 3.2 28.3 1.0
CB A:ASP85 3.2 26.8 1.0
ZN A:ZN602 3.5 25.6 1.0
CB A:ASP36 3.6 30.1 1.0
O7 A:VPD604 3.8 34.5 1.0
ND2 A:ASN245 4.1 28.8 1.0
OD1 A:ASP85 4.1 25.0 1.0
O3 A:VPD604 4.2 24.4 1.0
NH2 A:ARG395 4.2 26.2 1.0
C6 A:VPD604 4.2 28.7 1.0
OD1 A:ASP36 4.2 26.8 1.0
CE1 A:HIS220 4.2 29.2 1.0
ND1 A:HIS38 4.2 23.4 1.0
CA A:ASP36 4.3 28.6 1.0
CG A:HIS38 4.3 25.4 1.0
C5 A:VPD604 4.3 25.7 1.0
NE2 A:HIS220 4.4 25.7 1.0
CD2 A:HIS118 4.4 20.0 1.0
O A:HIS243 4.6 30.0 1.0
CA A:HIS243 4.7 24.5 1.0
CA A:ASP85 4.7 25.1 1.0
NE2 A:HIS118 4.8 23.9 1.0

Zinc binding site 2 out of 8 in 7jv8

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Zinc binding site 2 out of 8 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35


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 35 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:25.6
occ:1.00
 OD1 A:ASN117 2.0 30.2 1.0
OD2 A:ASP85 2.1 33.5 1.0
NE2 A:HIS220 2.1 25.7 1.0
ND1 A:HIS243 2.1 20.8 1.0
O1 A:VPD604 2.2 30.2 1.0
O3 A:VPD604 2.6 24.4 1.0
P2 A:VPD604 2.9 28.6 1.0
CG A:ASP85 2.9 26.1 1.0
CE1 A:HIS243 2.9 25.7 1.0
CE1 A:HIS220 3.1 29.2 1.0
CD2 A:HIS220 3.1 24.1 1.0
CG A:ASN117 3.1 29.3 1.0
CG A:HIS243 3.2 24.8 1.0
OD1 A:ASP85 3.2 25.0 1.0
ZN A:ZN601 3.5 34.6 1.0
ND2 A:ASN117 3.6 26.4 1.0
CB A:HIS243 3.7 23.5 1.0
CA A:HIS243 3.8 24.5 1.0
O4 A:VPD604 4.0 23.0 1.0
OD2 A:ASP36 4.0 29.3 1.0
NE2 A:HIS243 4.1 23.9 1.0
ND1 A:HIS220 4.2 28.9 1.0
CD2 A:HIS118 4.2 20.0 1.0
CG A:HIS220 4.2 27.2 1.0
CD2 A:HIS243 4.2 25.4 1.0
C8 A:VPD604 4.3 26.7 1.0
CB A:ASP85 4.3 26.8 1.0
C5 A:VPD604 4.3 25.7 1.0
CB A:ASN117 4.4 26.9 1.0
O A:HIS243 4.5 30.0 1.0
N A:ASN117 4.5 30.1 1.0
C A:HIS243 4.7 24.6 1.0
N A:HIS243 4.7 28.5 1.0
NE2 A:HIS118 4.8 23.9 1.0

Zinc binding site 3 out of 8 in 7jv8

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Zinc binding site 3 out of 8 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35


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 35 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:47.4
occ:1.00
 OD2 B:ASP36 2.0 38.6 1.0
OD2 B:ASP85 2.1 46.7 1.0
NE2 B:HIS38 2.1 42.8 1.0
O B:HOH711 2.2 60.0 1.0
O1 B:VPD604 2.2 45.4 1.0
O4 B:VPD604 2.7 37.5 1.0
CG B:ASP85 3.0 34.3 1.0
P2 B:VPD604 3.0 39.6 1.0
CG B:ASP36 3.1 37.9 1.0
CE1 B:HIS38 3.1 35.6 1.0
CD2 B:HIS38 3.1 38.4 1.0
CB B:ASP85 3.2 31.9 1.0
ZN B:ZN602 3.5 41.8 1.0
CB B:ASP36 3.5 36.9 1.0
O7 B:VPD604 4.0 38.4 1.0
ND2 B:ASN245 4.0 75.6 1.0
O3 B:VPD604 4.1 34.5 1.0
OD1 B:ASP85 4.1 26.8 1.0
OD1 B:ASP36 4.2 30.0 1.0
C6 B:VPD604 4.2 36.1 1.0
ND1 B:HIS38 4.2 38.0 1.0
CA B:ASP36 4.2 33.4 1.0
CG B:HIS38 4.3 35.5 1.0
CE1 B:HIS220 4.3 31.3 1.0
NH2 B:ARG395 4.3 49.5 1.0
C5 B:VPD604 4.4 43.3 1.0
CD2 B:HIS118 4.4 40.5 1.0
NE2 B:HIS220 4.4 30.5 1.0
O B:HIS243 4.6 61.2 1.0
CA B:HIS243 4.7 51.8 1.0
CA B:ASP85 4.8 30.9 1.0
NE2 B:HIS118 4.9 46.8 1.0

Zinc binding site 4 out of 8 in 7jv8

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Zinc binding site 4 out of 8 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35


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 35 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:41.8
occ:1.00
 OD1 B:ASN117 2.0 32.8 1.0
OD2 B:ASP85 2.1 46.7 1.0
NE2 B:HIS220 2.1 30.5 1.0
ND1 B:HIS243 2.1 49.6 1.0
O1 B:VPD604 2.2 45.4 1.0
O3 B:VPD604 2.6 34.5 1.0
CG B:ASP85 2.9 34.3 1.0
CE1 B:HIS243 2.9 45.8 1.0
P2 B:VPD604 3.0 39.6 1.0
CE1 B:HIS220 3.1 31.3 1.0
CD2 B:HIS220 3.1 32.5 1.0
CG B:ASN117 3.1 38.5 1.0
OD1 B:ASP85 3.2 26.8 1.0
CG B:HIS243 3.2 45.6 1.0
ZN B:ZN601 3.5 47.4 1.0
ND2 B:ASN117 3.6 35.3 1.0
CB B:HIS243 3.7 44.6 1.0
CA B:HIS243 3.7 51.8 1.0
OD2 B:ASP36 3.9 38.6 1.0
O4 B:VPD604 3.9 37.5 1.0
NE2 B:HIS243 4.1 45.2 1.0
CD2 B:HIS118 4.1 40.5 1.0
ND1 B:HIS220 4.2 28.2 1.0
CG B:HIS220 4.2 35.4 1.0
CD2 B:HIS243 4.2 43.4 1.0
CB B:ASP85 4.3 31.9 1.0
C8 B:VPD604 4.4 47.1 1.0
C5 B:VPD604 4.4 43.3 1.0
CB B:ASN117 4.4 32.4 1.0
O B:HIS243 4.5 61.2 1.0
N B:ASN117 4.6 38.0 1.0
C B:HIS243 4.6 56.1 1.0
N B:HIS243 4.7 43.7 1.0
NE2 B:HIS118 4.8 46.8 1.0

Zinc binding site 5 out of 8 in 7jv8

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Zinc binding site 5 out of 8 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn601

b:52.8
occ:1.00
 OD2 C:ASP36 2.0 57.2 1.0
OD2 C:ASP85 2.0 43.7 1.0
NE2 C:HIS38 2.2 52.7 1.0
O C:HOH723 2.2 35.9 1.0
O1 C:VPD604 2.2 39.3 1.0
CG C:ASP85 2.9 34.9 1.0
O4 C:VPD604 3.0 31.6 1.0
CG C:ASP36 3.1 45.8 1.0
P2 C:VPD604 3.1 42.3 1.0
CE1 C:HIS38 3.1 56.6 1.0
CB C:ASP85 3.2 38.7 1.0
CD2 C:HIS38 3.2 43.9 1.0
ZN C:ZN602 3.4 38.2 1.0
CB C:ASP36 3.6 44.6 1.0
OD1 C:ASP85 4.1 28.5 1.0
O7 C:VPD604 4.1 46.6 1.0
O3 C:VPD604 4.1 28.3 1.0
OD1 C:ASP36 4.2 59.3 1.0
OD1 C:ASN245 4.2 53.5 1.0
NH2 C:ARG395 4.2 67.9 1.0
CE1 C:HIS220 4.2 43.1 1.0
ND1 C:HIS38 4.3 45.7 1.0
CA C:ASP36 4.3 47.6 1.0
C6 C:VPD604 4.3 47.7 1.0
CD2 C:HIS118 4.3 55.4 1.0
NE2 C:HIS220 4.3 50.1 1.0
CG C:HIS38 4.3 42.7 1.0
C5 C:VPD604 4.5 43.6 1.0
O C:HIS243 4.6 62.0 1.0
CA C:HIS243 4.7 48.4 1.0
CA C:ASP85 4.7 39.1 1.0
NE2 C:HIS118 4.8 55.4 1.0

Zinc binding site 6 out of 8 in 7jv8

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Zinc binding site 6 out of 8 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn602

b:38.2
occ:1.00
 OD1 C:ASN117 2.0 36.9 1.0
OD2 C:ASP85 2.0 43.7 1.0
NE2 C:HIS220 2.1 50.1 1.0
ND1 C:HIS243 2.1 56.0 1.0
O1 C:VPD604 2.2 39.3 1.0
O3 C:VPD604 2.6 28.3 1.0
CG C:ASP85 2.9 34.9 1.0
CE1 C:HIS243 3.0 55.9 1.0
P2 C:VPD604 3.0 42.3 1.0
CE1 C:HIS220 3.1 43.1 1.0
CD2 C:HIS220 3.1 52.5 1.0
CG C:ASN117 3.1 38.0 1.0
OD1 C:ASP85 3.2 28.5 1.0
CG C:HIS243 3.2 56.7 1.0
ZN C:ZN601 3.4 52.8 1.0
ND2 C:ASN117 3.6 37.8 1.0
CB C:HIS243 3.7 57.9 1.0
CA C:HIS243 3.8 48.4 1.0
OD2 C:ASP36 4.0 57.2 1.0
O4 C:VPD604 4.1 31.6 1.0
NE2 C:HIS243 4.1 61.5 1.0
CD2 C:HIS118 4.1 55.4 1.0
ND1 C:HIS220 4.2 46.1 1.0
CG C:HIS220 4.2 45.8 1.0
CD2 C:HIS243 4.2 59.6 1.0
CB C:ASP85 4.3 38.7 1.0
C5 C:VPD604 4.4 43.6 1.0
CB C:ASN117 4.4 35.4 1.0
C8 C:VPD604 4.5 44.3 1.0
O C:HIS243 4.5 62.0 1.0
N C:ASN117 4.6 41.2 1.0
C C:HIS243 4.7 52.5 1.0
N C:HIS243 4.7 48.5 1.0
NE2 C:HIS118 4.8 55.4 1.0

Zinc binding site 7 out of 8 in 7jv8

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Zinc binding site 7 out of 8 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:36.1
occ:1.00
 OD2 D:ASP36 2.0 23.4 1.0
OD2 D:ASP85 2.1 31.2 1.0
NE2 D:HIS38 2.1 34.2 1.0
O1 D:VPD604 2.2 29.9 1.0
O D:HOH708 2.3 34.2 1.0
CG D:ASP85 3.0 28.7 1.0
CE1 D:HIS38 3.1 36.0 1.0
CG D:ASP36 3.1 20.9 1.0
O4 D:VPD604 3.1 27.4 1.0
CD2 D:HIS38 3.1 36.4 1.0
P2 D:VPD604 3.2 28.7 1.0
CB D:ASP85 3.2 28.8 1.0
ZN D:ZN602 3.5 29.4 1.0
CB D:ASP36 3.5 24.4 1.0
O7 D:VPD604 3.8 24.2 1.0
ND2 D:ASN245 4.1 36.5 1.0
OD1 D:ASP85 4.1 27.2 1.0
C6 D:VPD604 4.2 21.5 1.0
OD1 D:ASP36 4.2 22.6 1.0
ND1 D:HIS38 4.2 37.7 1.0
NH2 D:ARG395 4.2 33.0 1.0
CA D:ASP36 4.2 22.6 1.0
CG D:HIS38 4.2 35.6 1.0
O3 D:VPD604 4.3 29.9 1.0
CE1 D:HIS220 4.3 24.5 1.0
CD2 D:HIS118 4.3 27.4 1.0
NE2 D:HIS220 4.4 25.1 1.0
C5 D:VPD604 4.4 24.6 1.0
O D:HIS243 4.7 30.8 1.0
CA D:HIS243 4.7 28.3 1.0
CA D:ASP85 4.7 26.5 1.0
NE2 D:HIS118 4.8 32.9 1.0

Zinc binding site 8 out of 8 in 7jv8

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Zinc binding site 8 out of 8 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:29.4
occ:1.00
 OD1 D:ASN117 2.0 35.9 1.0
OD2 D:ASP85 2.1 31.2 1.0
NE2 D:HIS220 2.1 25.1 1.0
ND1 D:HIS243 2.2 30.0 1.0
O1 D:VPD604 2.2 29.9 1.0
O3 D:VPD604 2.6 29.9 1.0
P2 D:VPD604 2.9 28.7 1.0
CG D:ASP85 2.9 28.7 1.0
CE1 D:HIS243 3.0 35.6 1.0
CE1 D:HIS220 3.1 24.5 1.0
CD2 D:HIS220 3.1 28.4 1.0
CG D:ASN117 3.1 35.2 1.0
OD1 D:ASP85 3.2 27.2 1.0
CG D:HIS243 3.3 27.8 1.0
ZN D:ZN601 3.5 36.1 1.0
ND2 D:ASN117 3.6 32.6 1.0
CB D:HIS243 3.7 27.3 1.0
CA D:HIS243 3.8 28.3 1.0
OD2 D:ASP36 3.9 23.4 1.0
O4 D:VPD604 4.0 27.4 1.0
CD2 D:HIS118 4.1 27.4 1.0
NE2 D:HIS243 4.2 23.5 1.0
ND1 D:HIS220 4.2 30.1 1.0
CG D:HIS220 4.2 31.1 1.0
CB D:ASP85 4.3 28.8 1.0
C8 D:VPD604 4.3 24.6 1.0
CD2 D:HIS243 4.3 27.7 1.0
C5 D:VPD604 4.3 24.6 1.0
CB D:ASN117 4.4 30.7 1.0
O D:HIS243 4.5 30.8 1.0
N D:ASN117 4.6 31.2 1.0
C D:HIS243 4.6 29.1 1.0
N D:HIS243 4.7 26.3 1.0
NE2 D:HIS118 4.8 32.9 1.0

Reference:

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
Page generated: Tue Oct 29 21:06:15 2024

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