Receptor
PDB id Resolution Class Description Source Keywords
6TWA 2 Å EC: 3.1.3.5 HUMAN CD73 (ECTO 5'-NUCLEOTIDASE) IN COMPLEX WITH PSB12646 ( DERIVATIVE, COMPOUND 20 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:604;
 Part of Protein;
 none;
 submit data
40.078 Ca [Ca+2...
O02 A:603;
 Valid;
 none;
 Ki = 15.5 nM
455.258 C11 H19 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: O02; Similar ligands found: 154
No: Ligand ECFP6 Tc MDL keys Tc
1 O02 1 1
2 A12 0.6875 0.960526
3 AP2 0.6875 0.960526
4 O05 0.621053 0.870588
5 APC 0.573034 0.960526
6 ADV 0.566667 0.935065
7 RBY 0.566667 0.935065
8 ACP 0.561798 0.947368
9 AMP 0.547619 0.894737
10 A 0.547619 0.894737
11 A2D 0.528736 0.896104
12 ABM 0.528736 0.848101
13 45A 0.528736 0.848101
14 HFD 0.526882 0.875
15 JSQ 0.526882 0.875
16 AMP MG 0.523256 0.857143
17 BA3 0.516854 0.896104
18 CA0 0.516484 0.873418
19 AU1 0.516484 0.922078
20 ADX 0.516484 0.811765
21 APC MG 0.516129 0.896104
22 6AD 0.515789 0.843373
23 B4P 0.511111 0.896104
24 AP5 0.511111 0.896104
25 ADP 0.511111 0.921053
26 SRA 0.505747 0.85
27 AT4 0.505495 0.886076
28 AN2 0.505495 0.934211
29 ACQ 0.505263 0.947368
30 GP2 0.505263 0.9125
31 AVV 0.50505 0.876543
32 M33 0.5 0.884615
33 AD9 0.5 0.897436
34 NYZ 0.494737 0.888889
35 50T 0.494624 0.884615
36 KG4 0.494624 0.873418
37 HEJ 0.494624 0.921053
38 ATP 0.494624 0.921053
39 9ZD 0.49 0.864198
40 9ZA 0.49 0.864198
41 6YZ 0.489796 0.947368
42 ANP 0.489583 0.922078
43 AR6 0.489362 0.896104
44 5FA 0.489362 0.921053
45 APR 0.489362 0.896104
46 PRX 0.489362 0.82716
47 AQP 0.489362 0.921053
48 ADP MG 0.48913 0.87013
49 ADP BEF 0.48913 0.87013
50 V2G 0.484536 0.876543
51 ATP MG 0.484211 0.87013
52 AGS 0.484211 0.875
53 ADP PO3 0.484211 0.87013
54 71V 0.483516 0.864198
55 T99 0.474227 0.886076
56 GAP 0.474227 0.82716
57 TAT 0.474227 0.886076
58 SON 0.473118 0.910256
59 TAD 0.472727 0.888889
60 EO7 0.472527 0.755556
61 5AL 0.469388 0.860759
62 8LE 0.469388 0.829268
63 QA7 0.465347 0.829268
64 MAP 0.465347 0.898734
65 ANP MG 0.464646 0.884615
66 ATF 0.464646 0.886076
67 BEF ADP 0.463918 0.848101
68 OZV 0.460784 0.896104
69 SRP 0.46 0.8625
70 8LH 0.46 0.839506
71 A3R 0.456311 0.8875
72 4AD 0.456311 0.875
73 AMO 0.456311 0.886076
74 HQG 0.455446 0.909091
75 AHX 0.451923 0.876543
76 DLL 0.451923 0.860759
77 DAL AMP 0.45098 0.8375
78 A22 0.45098 0.909091
79 8LQ 0.45098 0.8625
80 VO4 ADP 0.45 0.873418
81 ALF ADP 0.45 0.807229
82 25A 0.446602 0.896104
83 OOB 0.446602 0.860759
84 8QN 0.446602 0.860759
85 5SV 0.446602 0.809524
86 LMS 0.444444 0.790698
87 B5V 0.443396 0.839506
88 WAQ 0.443396 0.864198
89 PAJ 0.442308 0.821429
90 ADQ 0.442308 0.873418
91 A1R 0.442308 0.8875
92 1ZZ 0.439252 0.802326
93 TXA 0.439252 0.8625
94 NB8 0.439252 0.876543
95 JNT 0.438095 0.897436
96 00A 0.438095 0.819277
97 2FA 0.435294 0.753086
98 MYR AMP 0.435185 0.781609
99 9X8 0.433962 0.851852
100 3UK 0.433962 0.85
101 OAD 0.433962 0.873418
102 5AS 0.431579 0.747253
103 PR8 0.429907 0.833333
104 LAD 0.429907 0.843373
105 4TC 0.42735 0.876543
106 KMQ 0.427273 0.8625
107 DZD 0.42623 0.888889
108 3OD 0.425926 0.873418
109 BIS 0.425926 0.864198
110 FYA 0.425926 0.860759
111 ME8 0.425926 0.802326
112 PTJ 0.425926 0.831325
113 6MZ 0.425532 0.858974
114 XAH 0.423423 0.845238
115 G2P 0.423077 0.9125
116 PGS 0.42268 0.819277
117 UP5 0.422414 0.851852
118 25L 0.422018 0.909091
119 ADP BMA 0.420561 0.85
120 AMP DBH 0.419643 0.82716
121 AOC 0.419355 0.759494
122 9SN 0.418182 0.809524
123 NIA 0.417582 0.785714
124 LAQ 0.417391 0.802326
125 G3A 0.415929 0.876543
126 IMO 0.414894 0.857143
127 B5M 0.414414 0.829268
128 ATP A 0.414414 0.858974
129 ATP A A A 0.414414 0.858974
130 FA5 0.414414 0.8625
131 B5Y 0.414414 0.829268
132 LPA AMP 0.413793 0.781609
133 GCP 0.413462 0.9
134 JB6 0.412844 0.841463
135 AFH 0.412281 0.843373
136 ARG AMP 0.412281 0.813953
137 GA7 0.412281 0.8625
138 G5P 0.412281 0.876543
139 C2R 0.411111 0.835443
140 AMZ 0.411111 0.846154
141 ITT 0.408163 0.87013
142 4UV 0.40708 0.829268
143 G5A 0.405941 0.766667
144 6C6 0.405941 0.8625
145 AHZ 0.405172 0.761364
146 ADN 0.404762 0.779221
147 RAB 0.404762 0.779221
148 XYA 0.404762 0.779221
149 H1Q 0.40404 0.835443
150 AIR 0.402299 0.831169
151 YLP 0.401709 0.804598
152 7MD 0.4 0.845238
153 7RA 0.4 0.907895
154 4UU 0.4 0.829268
Similar Ligands (3D)
Ligand no: 1; Ligand: O02; Similar ligands found: 7
No: Ligand Similarity coefficient
1 GDP 0.9303
2 7DD 0.9014
3 M7G 0.8923
4 DAT 0.8898
5 5GP 0.8851
6 GJV 0.8793
7 8GD 0.8740
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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