Receptor
PDB id Resolution Class Description Source Keywords
6TWF 2.5 Å EC: 3.1.3.5 HUMAN CD73 (ECTO 5'-NUCLEOTIDASE) IN COMPLEX WITH PSB12604 ( DERIVATIVE, COMPOUND 21 IN PUBLICATION) IN THE CLOSED STATE HOMO SAPIENS NUCLEOTIDE ANALOG EN 5NT COMPLEX HYDROLASE
Ref.: 2-SUBSTITUTED ALPHA , BETA-METHYLENE-ADP DERIVATIVE COMPETITIVE ECTO-5'-NUCLEOTIDASE (CD73) INHIBITORS VARIABLE BINDING MODES. J.MED.CHEM. V. 63 2941 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN A:602;
A:601;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
65.409 Zn [Zn+2...
CA A:603;
 Part of Protein;
 none;
 submit data
40.078 Ca [Ca+2...
O05 A:604;
 Valid;
 none;
 Ki = 184 nM
510.356 C15 H26 N7 O9 P2 c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6Z9D 1.9 Å EC: 3.1.3.5 HUMAN ECTO-5'-NUCLEOTIDASE (CD73) IN COMPLEX WITH AOPCP DERI AB680 (COMPOUND 55 IN PUBLICATION) IN THE CLOSED FORM (CRYSI II) HOMO SAPIENS ZINC ENZYME NUCLEOTIDE ANALOG INHIBITOR ARCUS BIOSCIENCESHYDROLASE
Ref.: DISCOVERY OF AB680: A POTENT AND SELECTIVE INHIBITO CD73. J.MED.CHEM. V. 63 11448 2020
Members (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 6XUE ic50 = 19 nM O1H C24 H15 Cl N8 c1cc(ccc1C....
2 4H2F - ADN C10 H13 N5 O4 c1nc(c2c(n....
3 6XUG ic50 = 12 nM O1Q C23 H16 Cl N7 Cc1cccc(c1....
4 6TVG Ki = 88.4 nM AP2 C11 H17 N5 O9 P2 c1nc(c2c(n....
5 6XUQ Ki = 88.4 nM O1T C20 H24 Cl F N4 O9 P2 C[C@@H](c1....
6 6TWF Ki = 184 nM O05 C15 H26 N7 O9 P2 c1nc2c(nc(....
7 7JV8 ic50 = 0.25 nM VPD C19 H29 Cl N5 O9 P COC[C@](CO....
8 4H2G - ADN C10 H13 N5 O4 c1nc(c2c(n....
9 6TW0 Ki = 38.8 nM NYZ C11 H17 N5 O10 P2 c1nc2c(n1[....
10 4H2B - 0XE C21 H18 O11 c1ccc(cc1)....
11 6TWA Ki = 15.5 nM O02 C11 H19 N7 O9 P2 c1nc2c(nc(....
12 6Z9B ic50 = 0.7 nM QCQ C18 H21 Cl F N5 O8 P2 c1ccc(cc1)....
13 4H1Y - 0YQ C17 H23 N5 O11 C1=CN(C(=O....
14 4H2I - A12 C11 H17 N5 O9 P2 c1nc(c2c(n....
15 6Z9D Ki = 5 pM QDH C20 H24 Cl F N4 O9 P2 C[C@@H](c1....
70% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 6XUE ic50 = 19 nM O1H C24 H15 Cl N8 c1cc(ccc1C....
2 4H2F - ADN C10 H13 N5 O4 c1nc(c2c(n....
3 6XUG ic50 = 12 nM O1Q C23 H16 Cl N7 Cc1cccc(c1....
4 6TVG Ki = 88.4 nM AP2 C11 H17 N5 O9 P2 c1nc(c2c(n....
5 6XUQ Ki = 88.4 nM O1T C20 H24 Cl F N4 O9 P2 C[C@@H](c1....
6 6TWF Ki = 184 nM O05 C15 H26 N7 O9 P2 c1nc2c(nc(....
7 7JV8 ic50 = 0.25 nM VPD C19 H29 Cl N5 O9 P COC[C@](CO....
8 4H2G - ADN C10 H13 N5 O4 c1nc(c2c(n....
9 6TW0 Ki = 38.8 nM NYZ C11 H17 N5 O10 P2 c1nc2c(n1[....
10 4H2B - 0XE C21 H18 O11 c1ccc(cc1)....
11 6TWA Ki = 15.5 nM O02 C11 H19 N7 O9 P2 c1nc2c(nc(....
12 6Z9B ic50 = 0.7 nM QCQ C18 H21 Cl F N5 O8 P2 c1ccc(cc1)....
13 4H1Y - 0YQ C17 H23 N5 O11 C1=CN(C(=O....
14 4H2I - A12 C11 H17 N5 O9 P2 c1nc(c2c(n....
15 6Z9D Ki = 5 pM QDH C20 H24 Cl F N4 O9 P2 C[C@@H](c1....
50% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 6XUE ic50 = 19 nM O1H C24 H15 Cl N8 c1cc(ccc1C....
2 4H2F - ADN C10 H13 N5 O4 c1nc(c2c(n....
3 6XUG ic50 = 12 nM O1Q C23 H16 Cl N7 Cc1cccc(c1....
4 6TVG Ki = 88.4 nM AP2 C11 H17 N5 O9 P2 c1nc(c2c(n....
5 6XUQ Ki = 88.4 nM O1T C20 H24 Cl F N4 O9 P2 C[C@@H](c1....
6 6TWF Ki = 184 nM O05 C15 H26 N7 O9 P2 c1nc2c(nc(....
7 7JV8 ic50 = 0.25 nM VPD C19 H29 Cl N5 O9 P COC[C@](CO....
8 4H2G - ADN C10 H13 N5 O4 c1nc(c2c(n....
9 6TW0 Ki = 38.8 nM NYZ C11 H17 N5 O10 P2 c1nc2c(n1[....
10 4H2B - 0XE C21 H18 O11 c1ccc(cc1)....
11 6TWA Ki = 15.5 nM O02 C11 H19 N7 O9 P2 c1nc2c(nc(....
12 6Z9B ic50 = 0.7 nM QCQ C18 H21 Cl F N5 O8 P2 c1ccc(cc1)....
13 4H1Y - 0YQ C17 H23 N5 O11 C1=CN(C(=O....
14 4H2I - A12 C11 H17 N5 O9 P2 c1nc(c2c(n....
15 6Z9D Ki = 5 pM QDH C20 H24 Cl F N4 O9 P2 C[C@@H](c1....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: O05; Similar ligands found: 71
No: Ligand ECFP6 Tc MDL keys Tc
1 O05 1 1
2 O02 0.621053 0.870588
3 AP2 0.580645 0.879518
4 A12 0.580645 0.879518
5 APC 0.490196 0.879518
6 ADV 0.485437 0.857143
7 RBY 0.485437 0.857143
8 JSQ 0.480769 0.804598
9 HFD 0.480769 0.804598
10 ACP 0.480392 0.86747
11 A 0.463918 0.819277
12 AMP 0.463918 0.819277
13 AVV 0.463636 0.827586
14 6AD 0.457944 0.777778
15 ABM 0.45 0.77907
16 A2D 0.45 0.843373
17 45A 0.45 0.77907
18 SRA 0.444444 0.781609
19 AMP MG 0.444444 0.807229
20 ADX 0.442308 0.75
21 CA0 0.442308 0.802326
22 BA3 0.441176 0.843373
23 ADP 0.436893 0.843373
24 AP5 0.436893 0.843373
25 B4P 0.436893 0.843373
26 ACQ 0.435185 0.86747
27 GP2 0.435185 0.83908
28 AN2 0.432692 0.833333
29 AT4 0.432692 0.813953
30 V2G 0.431193 0.848837
31 APC MG 0.429907 0.843373
32 M33 0.428571 0.811765
33 AU1 0.428571 0.823529
34 71V 0.427184 0.795455
35 NYZ 0.425926 0.818182
36 KG4 0.424528 0.802326
37 ATP 0.424528 0.843373
38 HEJ 0.424528 0.843373
39 50T 0.424528 0.811765
40 6YZ 0.423423 0.86747
41 AR6 0.420561 0.821429
42 APR 0.420561 0.821429
43 PRX 0.420561 0.802326
44 AQP 0.420561 0.843373
45 5FA 0.420561 0.843373
46 ADP MG 0.419048 0.819277
47 ADP BEF 0.419048 0.819277
48 EO7 0.417476 0.683673
49 ADP PO3 0.416667 0.819277
50 ATP MG 0.416667 0.819277
51 AGS 0.416667 0.804598
52 AD9 0.416667 0.823529
53 TAD 0.414634 0.818182
54 ATF 0.414414 0.813953
55 9ZD 0.412281 0.775281
56 9ZA 0.412281 0.775281
57 T99 0.409091 0.813953
58 GAP 0.409091 0.823529
59 TAT 0.409091 0.813953
60 ANP 0.409091 0.823529
61 4AD 0.408696 0.847059
62 SON 0.40566 0.835294
63 5AL 0.405405 0.790698
64 8LE 0.405405 0.764045
65 JNT 0.405172 0.86747
66 ANP MG 0.401786 0.811765
67 OAD 0.401709 0.802326
68 9X8 0.401709 0.784091
69 BEF ADP 0.4 0.8
70 OZV 0.4 0.821429
71 OOB 0.4 0.811765
Similar Ligands (3D)
Ligand no: 1; Ligand: O05; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6Z9D; Ligand: QDH; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 6z9d.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6Z9D; Ligand: QDH; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 6z9d.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
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