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 (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: 7DD; Similar ligands found: 90
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 5FA 0.516854 0.985714
9 AQP 0.516854 0.985714
10 ACQ 0.516484 0.958333
11 A2D 0.505882 0.957747
12 B4P 0.505747 0.957747
13 AP5 0.505747 0.957747
14 AN2 0.5 0.971831
15 6YZ 0.5 0.958333
16 BA3 0.494253 0.957747
17 ACP 0.488889 0.958333
18 AR6 0.483516 0.957747
19 APR 0.483516 0.957747
20 AT4 0.483146 0.945205
21 6AD 0.478723 0.896104
22 SAP 0.478261 0.932432
23 AGS 0.478261 0.932432
24 M33 0.477778 0.944444
25 HFD 0.473118 0.932432
26 GDP 0.468085 0.906667
27 ANP 0.468085 0.958333
28 ADQ 0.464646 0.931507
29 AD9 0.462366 0.958333
30 ITT 0.461538 0.929577
31 A22 0.459184 0.971831
32 25L 0.456311 0.971831
33 AMP 0.453488 0.957143
34 A 0.453488 0.957143
35 T99 0.452632 0.945205
36 TAT 0.452632 0.945205
37 APC 0.451613 0.945205
38 PRX 0.451613 0.88
39 PAP 0.446809 0.971429
40 IDP 0.446809 0.905405
41 ATR 0.446809 0.957143
42 CA0 0.445652 0.931507
43 ADX 0.445652 0.860759
44 ATF 0.443299 0.945205
45 OAD 0.441176 0.931507
46 9X8 0.441176 0.906667
47 50T 0.44086 0.944444
48 2A5 0.43617 0.905405
49 4AD 0.435644 0.906667
50 3OD 0.432692 0.931507
51 8OD 0.427083 0.931507
52 AIR 0.426829 0.887324
53 25A 0.425743 0.957747
54 GTP 0.424242 0.906667
55 ABM 0.422222 0.90411
56 AAM 0.422222 0.957143
57 A1R 0.421569 0.894737
58 A3R 0.421569 0.894737
59 BIS 0.419048 0.92
60 5AL 0.418367 0.917808
61 7D3 0.417582 0.891892
62 00A 0.417476 0.87013
63 MGP 0.414141 0.871795
64 7CH 0.413043 0.9
65 A12 0.413043 0.945205
66 AP2 0.413043 0.945205
67 OOB 0.411765 0.917808
68 5SV 0.411765 0.835443
69 DAT 0.410526 0.891892
70 SRP 0.41 0.893333
71 6G0 0.41 0.871795
72 WAQ 0.409524 0.87013
73 NIA 0.409091 0.810127
74 AMO 0.407767 0.918919
75 GCP 0.405941 0.883117
76 1ZZ 0.40566 0.82716
77 GNH 0.40404 0.894737
78 DLL 0.403846 0.917808
79 AHX 0.403846 0.883117
80 C2R 0.402299 0.890411
81 AMZ 0.402299 0.902778
82 ADV 0.402062 0.918919
83 ADP PO3 0.402062 0.929577
84 RBY 0.402062 0.918919
85 SRA 0.4 0.905405
86 OMR 0.4 0.839506
87 3UK 0.4 0.905405
88 AU1 0.4 0.958333
89 ADP ALF 0.4 0.857143
90 ALF ADP 0.4 0.857143
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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