Receptor
PDB id Resolution Class Description Source Keywords
5EX5 1.9 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF HUMAN GRP78 (70KDA HEAT SHOCK PROTEIN 5 ATPASE DOMAIN IN COMPLEX WITH 7-DEAZA-ADP AND INORGANIC PHO HOMO SAPIENS CHAPERONE ATPASE DOMAIN NUCLEOTIDE-BINDING ENDOPLASMIC RE
Ref.: PROBING THE ATP SITE OF GRP78 WITH NUCLEOTIDE TRIPH ANALOGS. PLOS ONE V. 11 54862 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PO4 A:502;
B:502;
Invalid;
Invalid;
none;
none;
submit data
94.971 O4 P [O-]P...
7DD A:503;
B:503;
Valid;
Valid;
none;
none;
submit data
426.213 C11 H16 N4 O10 P2 c1cn(...
MG A:501;
B:501;
Invalid;
Invalid;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5EXW 1.9 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF HUMAN GRP78 (70KDA HEAT SHOCK PROTEIN 5 ATPASE DOMAIN IN COMPLEX WITH 7-DEAZA-ATP HOMO SAPIENS CHAPERONE ATPASE DOMAIN NUCLEOTIDE-BINDING ENDOPLASMIC RE
Ref.: PROBING THE ATP SITE OF GRP78 WITH NUCLEOTIDE TRIPH ANALOGS. PLOS ONE V. 11 54862 2016
Members (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 312 families.
1 5EY4 Kd = 0.00075 M DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
2 5EX5 - 7DD C11 H16 N4 O10 P2 c1cn(c2c1c....
3 5F1X Kd = 0.000000064 M ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 3LDP Kd = 2.41 uM 3P1 C20 H21 N7 O4 c1ccc2c(c1....
5 5F2R Kd = 0.000052 M ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
6 5EXW Kd = 0.000000064 M 7DT C11 H17 N4 O13 P3 c1cn(c2c1c....
7 3LDO - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
8 5EVZ Kd = 0.000000064 M ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
9 3LDL - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
10 5F0X - DAT C10 H15 N5 O9 P2 c1nc(c2c(n....
11 3IUC - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
12 6ZYH - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
70% Homology Family (74)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 261 families.
1 5EY4 Kd = 0.00075 M DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
2 5EX5 - 7DD C11 H16 N4 O10 P2 c1cn(c2c1c....
3 5F1X Kd = 0.000000064 M ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 3LDP Kd = 2.41 uM 3P1 C20 H21 N7 O4 c1ccc2c(c1....
5 5F2R Kd = 0.000052 M ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
6 5EXW Kd = 0.000000064 M 7DT C11 H17 N4 O13 P3 c1cn(c2c1c....
7 3LDO - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
8 5EVZ Kd = 0.000000064 M ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
9 3LDL - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
10 5F0X - DAT C10 H15 N5 O9 P2 c1nc(c2c(n....
11 3IUC - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
12 6ZYH - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
13 3GDQ - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
14 3JXU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
15 6G3R - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
16 6P2U - NO7 C13 H17 N5 O10 P2 C#CCNc1c2c....
17 1KAZ - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
18 1QQN - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
19 1NGH - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
20 1ATR - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
21 1NGC - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
22 1NGF - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
23 1BA1 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
24 3HSC - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
25 1BA0 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
26 1QQO - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
27 2QWL - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
28 1NGG - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
29 6B1I - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
30 1ATS - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
31 1NGJ - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
32 1NGE - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
33 1KAY - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
34 1BUP - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
35 1QQM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
36 6ZYJ - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
37 6B1N - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
38 1KAX - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
39 1NGD - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
40 2QWM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
41 2BUP - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
42 1NGA - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
43 4H5T - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
44 1NGI - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
45 6B1M - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
46 1HPM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
47 1NGB - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
48 5FPM - IWT C8 H6 N2 O S c1ccc(cc1)....
49 5FPE - 3TR C2 H4 N4 c1[nH]nc(n....
50 3I33 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
51 5FPD - PZA C5 H5 N3 O c1cnc(cn1)....
52 3FE1 - ADP MG n/a n/a
53 6ZYI - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
54 1HJO - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
55 6G3S - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
56 6FHK - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
57 3AY9 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
58 5AQX - KC7 C21 H23 N3 O4 c1ccc(cc1)....
59 5MKR Ki = 17 uM TI8 C22 H25 Cl N6 O5 C=CC(=O)OC....
60 5AR0 Kd = 720 nM GB8 C20 H21 N7 O4 c1cc2cc(cc....
61 5AQW - 5P7 C14 H17 N3 O3 c1ccc2c(c1....
62 5MKS Ki = 17 uM TI8 C22 H25 Cl N6 O5 C=CC(=O)OC....
63 3ATU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
64 1S3X - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
65 5AQZ Kd = 3.3 uM SGV C12 H15 N5 O5 c1c(c2c(nc....
66 2E8A - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
67 3ATV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
68 5AQY - ADN C10 H13 N5 O4 c1nc(c2c(n....
69 7A4V - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
70 6EOE - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
71 6EOF - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
72 3QFU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
73 6RZQ - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
74 6S02 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
50% Homology Family (85)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 214 families.
1 5EY4 Kd = 0.00075 M DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
2 5EX5 - 7DD C11 H16 N4 O10 P2 c1cn(c2c1c....
3 5F1X Kd = 0.000000064 M ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 3LDP Kd = 2.41 uM 3P1 C20 H21 N7 O4 c1ccc2c(c1....
5 5F2R Kd = 0.000052 M ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
6 5EXW Kd = 0.000000064 M 7DT C11 H17 N4 O13 P3 c1cn(c2c1c....
7 3LDO - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
8 5EVZ Kd = 0.000000064 M ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
9 3LDL - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
10 5F0X - DAT C10 H15 N5 O9 P2 c1nc(c2c(n....
11 3IUC - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
12 6ZYH - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
13 3GDQ - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
14 3JXU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
15 6G3R - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
16 6P2U - NO7 C13 H17 N5 O10 P2 C#CCNc1c2c....
17 2V7Y - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
18 1KAZ - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
19 1QQN - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
20 1NGH - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
21 1ATR - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
22 1NGC - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
23 1NGF - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
24 1BA1 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
25 3HSC - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
26 1BA0 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
27 1QQO - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
28 2QWL - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
29 1NGG - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
30 6B1I - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
31 1ATS - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
32 1NGJ - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
33 1NGE - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
34 1KAY - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
35 1BUP - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
36 1QQM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
37 6ZYJ - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
38 6B1N - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
39 1KAX - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
40 1NGD - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
41 2QWM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
42 2BUP - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
43 1NGA - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
44 4H5T - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
45 1NGI - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
46 6B1M - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
47 1HPM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
48 1NGB - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
49 5FPM - IWT C8 H6 N2 O S c1ccc(cc1)....
50 5FPE - 3TR C2 H4 N4 c1[nH]nc(n....
51 3I33 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
52 5FPD - PZA C5 H5 N3 O c1cnc(cn1)....
53 6GFA - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
54 6ASY - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
55 3FE1 - ADP MG n/a n/a
56 4GNI - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
57 6ZYI - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
58 1HJO - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
59 6G3S - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
60 6FHK - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
61 3AY9 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
62 5AQX - KC7 C21 H23 N3 O4 c1ccc(cc1)....
63 5MKR Ki = 17 uM TI8 C22 H25 Cl N6 O5 C=CC(=O)OC....
64 5AR0 Kd = 720 nM GB8 C20 H21 N7 O4 c1cc2cc(cc....
65 5AQW - 5P7 C14 H17 N3 O3 c1ccc2c(c1....
66 5MKS Ki = 17 uM TI8 C22 H25 Cl N6 O5 C=CC(=O)OC....
67 3ATU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
68 1S3X - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
69 5AQZ Kd = 3.3 uM SGV C12 H15 N5 O5 c1c(c2c(nc....
70 2E8A - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
71 3ATV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
72 5AQY - ADN C10 H13 N5 O4 c1nc(c2c(n....
73 4JN4 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
74 4JNE - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
75 7A4V - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
76 6EOE - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
77 6EOF - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
78 5OBY - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
79 5OBW - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
80 5OBV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
81 5OBU - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
82 5FPN - KYD C6 H8 N2 O2 Cc1c(c(n[n....
83 3QFU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
84 6RZQ - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
85 6S02 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 7DD; Similar ligands found: 109
No: Ligand ECFP6 Tc MDL keys Tc
1 7DD 1 1
2 7DT 0.901408 1
3 TBN 0.661765 0.842857
4 ADP 0.578313 0.985714
5 MTH 0.564103 0.77027
6 ATP 0.522727 0.985714
7 HEJ 0.522727 0.985714
8 AQP 0.516854 0.985714
9 5FA 0.516854 0.985714
10 ACQ 0.516484 0.958333
11 A2D 0.505882 0.957747
12 AP5 0.505747 0.957747
13 B4P 0.505747 0.957747
14 6YZ 0.5 0.958333
15 AN2 0.5 0.971831
16 BA3 0.494253 0.957747
17 ACP 0.488889 0.958333
18 APR 0.483516 0.957747
19 AR6 0.483516 0.957747
20 AT4 0.483146 0.945205
21 NO7 0.479167 0.918919
22 6AD 0.478723 0.896104
23 QBQ 0.478723 0.918919
24 AGS 0.478261 0.932432
25 M33 0.477778 0.944444
26 HFD 0.473118 0.932432
27 JSQ 0.473118 0.932432
28 GDP 0.468085 0.906667
29 ANP 0.468085 0.958333
30 ADQ 0.464646 0.931507
31 AD9 0.462366 0.958333
32 ITT 0.461538 0.929577
33 A22 0.459184 0.971831
34 25L 0.456311 0.971831
35 AMP 0.453488 0.957143
36 A 0.453488 0.957143
37 TAT 0.452632 0.945205
38 T99 0.452632 0.945205
39 APC 0.451613 0.945205
40 PRX 0.451613 0.88
41 HQG 0.44898 0.971831
42 PAP 0.446809 0.971429
43 ATR 0.446809 0.957143
44 IDP 0.446809 0.905405
45 ADX 0.445652 0.860759
46 CA0 0.445652 0.931507
47 ATF 0.443299 0.945205
48 OAD 0.441176 0.931507
49 9X8 0.441176 0.906667
50 KG4 0.44086 0.931507
51 50T 0.44086 0.944444
52 2A5 0.43617 0.905405
53 4AD 0.435644 0.906667
54 3OD 0.432692 0.931507
55 AMP MG 0.431818 0.915493
56 8LQ 0.43 0.893333
57 8OD 0.427083 0.931507
58 AIR 0.426829 0.887324
59 25A 0.425743 0.957747
60 GTP 0.424242 0.906667
61 ABM 0.422222 0.90411
62 AAM 0.422222 0.957143
63 45A 0.422222 0.90411
64 A3R 0.421569 0.894737
65 A1R 0.421569 0.894737
66 KMQ 0.420561 0.918919
67 ADP MG 0.419355 0.929577
68 ADP BEF 0.419355 0.929577
69 BIS 0.419048 0.92
70 5AL 0.418367 0.917808
71 8LE 0.418367 0.881579
72 7D3 0.417582 0.891892
73 JNT 0.417476 0.931507
74 00A 0.417476 0.87013
75 QA7 0.415842 0.881579
76 MGP 0.414141 0.871795
77 AP2 0.413043 0.945205
78 A12 0.413043 0.945205
79 7CH 0.413043 0.9
80 OZV 0.411765 0.957747
81 OOB 0.411765 0.917808
82 5SV 0.411765 0.835443
83 DAT 0.410526 0.891892
84 6G0 0.41 0.871795
85 8LH 0.41 0.893333
86 SRP 0.41 0.893333
87 WAQ 0.409524 0.87013
88 NIA 0.409091 0.810127
89 CZF 0.408163 0.917808
90 AMO 0.407767 0.918919
91 GCP 0.405941 0.883117
92 1ZZ 0.40566 0.82716
93 GNH 0.40404 0.894737
94 AHX 0.403846 0.883117
95 DLL 0.403846 0.917808
96 AMZ 0.402299 0.902778
97 C2R 0.402299 0.890411
98 6MZ 0.402174 0.916667
99 ADP PO3 0.402062 0.929577
100 APC MG 0.402062 0.90411
101 ATP MG 0.402062 0.929577
102 ADV 0.402062 0.918919
103 RBY 0.402062 0.918919
104 ANP MG 0.4 0.917808
105 3UK 0.4 0.905405
106 ALF ADP 0.4 0.857143
107 SRA 0.4 0.905405
108 OMR 0.4 0.839506
109 AU1 0.4 0.958333
Similar Ligands (3D)
Ligand no: 1; Ligand: 7DD; Similar ligands found: 11
No: Ligand Similarity coefficient
1 ADP AF3 0.9519
2 GDP MG 0.9356
3 GP2 0.9262
4 M7G 0.9218
5 O02 0.9014
6 CUU 0.8868
7 NWZ 0.8834
8 IMP 0.8812
9 5GP 0.8775
10 NX8 0.8755
11 FMP 0.8693
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5EXW; Ligand: 7DT; Similar sites found with APoc: 4
This union binding pocket(no: 1) in the query (biounit: 5exw.bio2) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 1SQK ADP 3.25
2 3MN7 ATP 8.16327
3 6I4M ADP 11.3757
4 5LJW ANP 14.121
Pocket No.: 2; Query (leader) PDB : 5EXW; Ligand: 7DT; 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: 5exw.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
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