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 = 0.15 uM
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 (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 253 families.
1 5EY4 Kd = 0.75 mM DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
2 5EX5 - 7DD C11 H16 N4 O10 P2 c1cn(c2c1c....
3 5F1X Kd = 0.78 uM 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 = 0.052 mM ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
6 5EXW Kd = 0.15 uM 7DT C11 H17 N4 O13 P3 c1cn(c2c1c....
7 3LDO - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
8 5EVZ Kd = 0.27 uM 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....
70% Homology Family (67)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 209 families.
1 5EY4 Kd = 0.75 mM DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
2 5EX5 - 7DD C11 H16 N4 O10 P2 c1cn(c2c1c....
3 5F1X Kd = 0.78 uM 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 = 0.052 mM ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
6 5EXW Kd = 0.15 uM 7DT C11 H17 N4 O13 P3 c1cn(c2c1c....
7 3LDO - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
8 5EVZ Kd = 0.27 uM 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 3GDQ - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
13 3JXU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
14 6G3R - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
15 1KAZ - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
16 1QQN - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
17 1NGH - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
18 1ATR - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
19 1NGC - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
20 1NGF - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
21 1BA1 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
22 3HSC - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
23 1BA0 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
24 1QQO - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
25 2QWL - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
26 1NGG - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
27 6B1I - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
28 1ATS - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
29 1NGJ - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
30 1NGE - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
31 1KAY - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
32 1BUP - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
33 1QQM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
34 6B1N - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
35 1KAX - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
36 1NGD - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
37 2QWM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
38 2BUP - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
39 1NGA - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
40 4H5T - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
41 1NGI - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
42 6B1M - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
43 1HPM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
44 1NGB - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
45 5FPM - IWT C8 H6 N2 O S c1ccc(cc1)....
46 5FPE - 3TR C2 H4 N4 c1[nH]nc(n....
47 3I33 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
48 5FPD - PZA C5 H5 N3 O c1cnc(cn1)....
49 3FE1 - ADP MG n/a n/a
50 1HJO - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
51 6G3S - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
52 6FHK - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
53 3AY9 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
54 5AQX - KC7 C21 H23 N3 O4 c1ccc(cc1)....
55 5MKR Ki = 17 uM TI8 C22 H25 Cl N6 O5 C=CC(=O)OC....
56 5AR0 Kd = 720 nM GB8 C20 H21 N7 O4 c1cc2cc(cc....
57 5AQW - 5P7 C14 H17 N3 O3 c1ccc2c(c1....
58 5MKS Ki = 17 uM TI8 C22 H25 Cl N6 O5 C=CC(=O)OC....
59 3ATU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
60 1S3X - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
61 5AQZ Kd = 3.3 uM SGV C12 H15 N5 O5 c1c(c2c(nc....
62 2E8A - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
63 3ATV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
64 5AQY - ADN C10 H13 N5 O4 c1nc(c2c(n....
65 6EOE - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
66 6EOF - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
67 3QFU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
50% Homology Family (77)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 173 families.
1 5EY4 Kd = 0.75 mM DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
2 5EX5 - 7DD C11 H16 N4 O10 P2 c1cn(c2c1c....
3 5F1X Kd = 0.78 uM 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 = 0.052 mM ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
6 5EXW Kd = 0.15 uM 7DT C11 H17 N4 O13 P3 c1cn(c2c1c....
7 3LDO - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
8 5EVZ Kd = 0.27 uM 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 3GDQ - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
13 3JXU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
14 6G3R - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
15 2V7Y - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
16 1KAZ - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
17 1QQN - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
18 1NGH - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
19 1ATR - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
20 1NGC - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
21 1NGF - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
22 1BA1 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
23 3HSC - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
24 1BA0 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
25 1QQO - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
26 2QWL - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
27 1NGG - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
28 6B1I - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
29 1ATS - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
30 1NGJ - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
31 1NGE - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
32 1KAY - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
33 1BUP - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
34 1QQM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
35 6B1N - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
36 1KAX - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
37 1NGD - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
38 2QWM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
39 2BUP - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
40 1NGA - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
41 4H5T - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
42 1NGI - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
43 6B1M - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
44 1HPM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
45 1NGB - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
46 5FPM - IWT C8 H6 N2 O S c1ccc(cc1)....
47 5FPE - 3TR C2 H4 N4 c1[nH]nc(n....
48 3I33 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
49 5FPD - PZA C5 H5 N3 O c1cnc(cn1)....
50 6ASY - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
51 3FE1 - ADP MG n/a n/a
52 4GNI - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
53 4JN4 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
54 4JNE - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
55 5OBY - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
56 5OBW - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
57 1HJO - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
58 6G3S - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
59 6FHK - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
60 3AY9 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
61 5AQX - KC7 C21 H23 N3 O4 c1ccc(cc1)....
62 5MKR Ki = 17 uM TI8 C22 H25 Cl N6 O5 C=CC(=O)OC....
63 5AR0 Kd = 720 nM GB8 C20 H21 N7 O4 c1cc2cc(cc....
64 5AQW - 5P7 C14 H17 N3 O3 c1ccc2c(c1....
65 5MKS Ki = 17 uM TI8 C22 H25 Cl N6 O5 C=CC(=O)OC....
66 3ATU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
67 1S3X - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
68 5AQZ Kd = 3.3 uM SGV C12 H15 N5 O5 c1c(c2c(nc....
69 2E8A - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
70 3ATV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
71 5AQY - ADN C10 H13 N5 O4 c1nc(c2c(n....
72 5OBV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
73 5OBU - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
74 6EOE - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
75 6EOF - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
76 5FPN - KYD C6 H8 N2 O2 Cc1c(c(n[n....
77 3QFU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 7DT; Similar ligands found: 82
No: Ligand ECFP6 Tc MDL keys Tc
1 7DT 1 1
2 7DD 0.901408 1
3 TBN 0.633803 0.842857
4 ATP 0.593023 0.985714
5 HEJ 0.593023 0.985714
6 5FA 0.586207 0.985714
7 AQP 0.586207 0.985714
8 MTH 0.54321 0.77027
9 AP5 0.54023 0.957747
10 B4P 0.54023 0.957747
11 HFD 0.538462 0.932432
12 BA3 0.528736 0.957747
13 ITT 0.52809 0.929577
14 ADP 0.522727 0.985714
15 6YZ 0.515789 0.958333
16 25L 0.514852 0.971831
17 SAP 0.51087 0.932432
18 AGS 0.51087 0.932432
19 A2D 0.505747 0.957747
20 ACQ 0.5 0.958333
21 GTP 0.484536 0.906667
22 APR 0.483871 0.957747
23 AR6 0.483871 0.957747
24 AN2 0.483516 0.971831
25 MGP 0.474227 0.871795
26 ACP 0.473118 0.958333
27 6G0 0.469388 0.871795
28 T99 0.46875 0.945205
29 TAT 0.46875 0.945205
30 AT4 0.467391 0.945205
31 ADQ 0.465347 0.931507
32 AD9 0.463158 0.958333
33 M33 0.462366 0.944444
34 A22 0.46 0.971831
35 MGO 0.454545 0.848101
36 ANP 0.453608 0.958333
37 7D4 0.446809 0.891892
38 H6Y 0.444444 0.931507
39 9X8 0.442308 0.906667
40 OAD 0.442308 0.931507
41 DTP 0.438776 0.891892
42 A 0.438202 0.957143
43 AMP 0.438202 0.957143
44 APC 0.4375 0.945205
45 PRX 0.4375 0.88
46 A3R 0.436893 0.894737
47 4AD 0.436893 0.906667
48 RGT 0.435185 0.945205
49 6AD 0.434343 0.896104
50 3OD 0.433962 0.931507
51 ADX 0.431579 0.860759
52 CA0 0.431579 0.931507
53 ATF 0.43 0.945205
54 HDV 0.43 0.88
55 GP3 0.428571 0.907895
56 50T 0.427083 0.944444
57 GDP 0.424242 0.906667
58 A1R 0.423077 0.894737
59 PRT 0.422018 0.917808
60 G5P 0.419643 0.907895
61 GSP 0.417476 0.860759
62 UP5 0.417391 0.906667
63 25A 0.413462 0.957747
64 AIR 0.411765 0.887324
65 G3A 0.410714 0.907895
66 AAM 0.408602 0.957143
67 ABM 0.408602 0.90411
68 BIS 0.407407 0.92
69 5AL 0.405941 0.917808
70 00A 0.40566 0.87013
71 IDP 0.40404 0.905405
72 PAP 0.40404 0.971429
73 ATR 0.40404 0.957143
74 GTA 0.403509 0.873418
75 OMR 0.401709 0.839506
76 OOB 0.4 0.917808
77 7CH 0.4 0.9
78 AP2 0.4 0.945205
79 T5A 0.4 0.829268
80 A12 0.4 0.945205
81 AVV 0.4 0.883117
82 5SV 0.4 0.835443
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: 3
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 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
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