Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
7DT B:501;
A:501;
 Valid;
Valid;
 none;
none;
 Kd = 0.000000064 M
506.193 C11 H17 N4 O13 P3 c1cn(...
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: 7DT; Similar ligands found: 95
No: Ligand ECFP6 Tc MDL keys Tc
1 7DT 1 1
2 7DD 0.901408 1
3 TBN 0.633803 0.842857
4 HEJ 0.593023 0.985714
5 ATP 0.593023 0.985714
6 5FA 0.586207 0.985714
7 AQP 0.586207 0.985714
8 QBQ 0.543478 0.918919
9 MTH 0.54321 0.77027
10 B4P 0.54023 0.957747
11 AP5 0.54023 0.957747
12 HFD 0.538462 0.932432
13 JSQ 0.538462 0.932432
14 BA3 0.528736 0.957747
15 ITT 0.52809 0.929577
16 ADP 0.522727 0.985714
17 6YZ 0.515789 0.958333
18 25L 0.514852 0.971831
19 AGS 0.51087 0.932432
20 A2D 0.505747 0.957747
21 ACQ 0.5 0.958333
22 GTP 0.484536 0.906667
23 AR6 0.483871 0.957747
24 APR 0.483871 0.957747
25 AN2 0.483516 0.971831
26 MGP 0.474227 0.871795
27 ACP 0.473118 0.958333
28 6G0 0.469388 0.871795
29 T99 0.46875 0.945205
30 CZF 0.46875 0.917808
31 TAT 0.46875 0.945205
32 AT4 0.467391 0.945205
33 ADQ 0.465347 0.931507
34 AD9 0.463158 0.958333
35 M33 0.462366 0.944444
36 A22 0.46 0.971831
37 MGO 0.454545 0.848101
38 ANP 0.453608 0.958333
39 HQG 0.45 0.971831
40 7D4 0.446809 0.891892
41 H6Y 0.444444 0.931507
42 9X8 0.442308 0.906667
43 OAD 0.442308 0.931507
44 DTP 0.438776 0.891892
45 AMP 0.438202 0.957143
46 A 0.438202 0.957143
47 APC 0.4375 0.945205
48 PRX 0.4375 0.88
49 A3R 0.436893 0.894737
50 4AD 0.436893 0.906667
51 NO7 0.435644 0.918919
52 RGT 0.435185 0.945205
53 6AD 0.434343 0.896104
54 3OD 0.433962 0.931507
55 ADX 0.431579 0.860759
56 CA0 0.431579 0.931507
57 HDV 0.43 0.88
58 ATF 0.43 0.945205
59 GP3 0.428571 0.907895
60 50T 0.427083 0.944444
61 KG4 0.427083 0.931507
62 GDP 0.424242 0.906667
63 A1R 0.423077 0.894737
64 KMQ 0.422018 0.918919
65 PRT 0.422018 0.917808
66 G5P 0.419643 0.907895
67 JNT 0.419048 0.931507
68 GSP 0.417476 0.860759
69 8LQ 0.417476 0.893333
70 UP5 0.417391 0.906667
71 25A 0.413462 0.957747
72 AIR 0.411765 0.887324
73 G3A 0.410714 0.907895
74 AAM 0.408602 0.957143
75 45A 0.408602 0.90411
76 ABM 0.408602 0.90411
77 BIS 0.407407 0.92
78 8LE 0.405941 0.881579
79 5AL 0.405941 0.917808
80 00A 0.40566 0.87013
81 ATR 0.40404 0.957143
82 IDP 0.40404 0.905405
83 PAP 0.40404 0.971429
84 QA7 0.403846 0.881579
85 GTA 0.403509 0.873418
86 AMP MG 0.402174 0.915493
87 OMR 0.401709 0.839506
88 AP2 0.4 0.945205
89 A12 0.4 0.945205
90 OOB 0.4 0.917808
91 OZV 0.4 0.957747
92 AVV 0.4 0.883117
93 T5A 0.4 0.829268
94 7CH 0.4 0.9
95 5SV 0.4 0.835443
Similar Ligands (3D)
Ligand no: 1; Ligand: 7DT; Similar ligands found: 6
No: Ligand Similarity coefficient
1 ADP AF3 0.9373
2 DAT 0.8871
3 ADP MG 0.8806
4 8QN 0.8706
5 ATP MG 0.8683
6 ADP ALF 0.8611
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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