Receptor
PDB id Resolution Class Description Source Keywords
3LDP 2.2 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF HUMAN GRP78 (70KDA HEAT SHOCK PROTEIN 5 ATPASE DOMAIN IN COMPLEX WITH SMALL MOLECULE INHIBITOR HOMO SAPIENS GRP78 HSP70 HSC70 CHAPERONE HEAT SHOCK PROTEIN FOLDINGBINDING ADENOSINE NUCLEOSIDE NUCLEOTIDE-BINDING STRESS SMALL MOLECULE INHIBITOR SELECTIVITY ENDOPLASMIC RETICULUPHOSPHOPROTEIN
Ref.: ADENOSINE-DERIVED INHIBITORS OF 78 KDA GLUCOSE REGU PROTEIN (GRP78) ATPASE: INSIGHTS INTO ISOFORM SELEC J.MED.CHEM. V. 54 4034 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3P1 A:408;
B:502;
Valid;
Valid;
none;
none;
Kd = 2.41 uM
423.425 C20 H21 N7 O4 c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5F1X 1.9 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF HUMAN GRP78 (70KDA HEAT SHOCK PROTEIN 5 ATPASE DOMAIN IN COMPLEX WITH 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 218 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 (59)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 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 1KAZ - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
15 1QQN - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
16 1NGH - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
17 1ATR - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
18 1NGC - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
19 1NGF - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
20 1BA1 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
21 3HSC - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
22 1BA0 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
23 1QQO - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
24 2QWL - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
25 1NGG - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
26 1ATS - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
27 1NGJ - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
28 1NGE - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
29 1KAY - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
30 1BUP - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
31 1QQM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
32 1KAX - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
33 1NGD - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
34 2QWM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
35 2BUP - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
36 1NGA - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
37 4H5T - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
38 1NGI - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
39 1HPM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
40 1NGB - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
41 5FPM - IWT C8 H6 N2 O S c1ccc(cc1)....
42 5FPE - 3TR C2 H4 N4 c1[nH]nc(n....
43 3I33 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
44 5FPD - PZA C5 H5 N3 O c1cnc(cn1)....
45 3FE1 - ADP MG n/a n/a
46 1HJO - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
47 3AY9 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
48 5AQX - KC7 C21 H23 N3 O4 c1ccc(cc1)....
49 5MKR Ki = 17 uM TI8 C22 H25 Cl N6 O5 C=CC(=O)OC....
50 5AR0 Kd = 720 nM GB8 C20 H21 N7 O4 c1cc2cc(cc....
51 5AQW - 5P7 C14 H17 N3 O3 c1ccc2c(c1....
52 5MKS Ki = 17 uM TI8 C22 H25 Cl N6 O5 C=CC(=O)OC....
53 3ATU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
54 1S3X - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
55 5AQZ Kd = 3.3 uM SGV C12 H15 N5 O5 c1c(c2c(nc....
56 2E8A - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
57 3ATV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
58 5AQY - ADN C10 H13 N5 O4 c1nc(c2c(n....
59 3QFU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
50% Homology Family (64)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 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 2V7Y - 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 1ATS - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
28 1NGJ - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
29 1NGE - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
30 1KAY - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
31 1BUP - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
32 1QQM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
33 1KAX - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
34 1NGD - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
35 2QWM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
36 2BUP - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
37 1NGA - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
38 4H5T - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
39 1NGI - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
40 1HPM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
41 1NGB - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
42 5FPM - IWT C8 H6 N2 O S c1ccc(cc1)....
43 5FPE - 3TR C2 H4 N4 c1[nH]nc(n....
44 3I33 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
45 5FPD - PZA C5 H5 N3 O c1cnc(cn1)....
46 3FE1 - ADP MG n/a n/a
47 4GNI - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
48 4JN4 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
49 4JNE - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
50 1HJO - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
51 3AY9 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
52 5AQX - KC7 C21 H23 N3 O4 c1ccc(cc1)....
53 5MKR Ki = 17 uM TI8 C22 H25 Cl N6 O5 C=CC(=O)OC....
54 5AR0 Kd = 720 nM GB8 C20 H21 N7 O4 c1cc2cc(cc....
55 5AQW - 5P7 C14 H17 N3 O3 c1ccc2c(c1....
56 5MKS Ki = 17 uM TI8 C22 H25 Cl N6 O5 C=CC(=O)OC....
57 3ATU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
58 1S3X - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
59 5AQZ Kd = 3.3 uM SGV C12 H15 N5 O5 c1c(c2c(nc....
60 2E8A - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
61 3ATV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
62 5AQY - ADN C10 H13 N5 O4 c1nc(c2c(n....
63 5FPN - KYD C6 H8 N2 O2 Cc1c(c(n[n....
64 3QFU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 3P1; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 3P1 1 1
2 3BK 0.568421 0.929577
3 GB8 0.564356 0.985075
4 TI8 0.464286 0.822785
5 3FD 0.46087 0.866667
6 3GO 0.45082 0.915493
7 3BH 0.44186 0.955224
8 3F5 0.44 0.863014
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5F1X; Ligand: ATP; Similar sites found: 83
This union binding pocket(no: 1) in the query (biounit: 5f1x.bio2) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2UYT ADP 0.0009667 0.42065 1.75
2 2UYT LRH 0.0009667 0.42065 1.75
3 4L80 OXL 0.02255 0.40458 2.01149
4 1P77 ATR 0.04651 0.40036 2.20588
5 5U7W ADE 0.03347 0.4112 2.25
6 5TE1 7A2 0.02131 0.41439 3
7 4B1X ATP 0.000000002977 0.6859 3.25
8 4B1V ATP 0.00000002709 0.59769 3.25
9 2V51 ATP 0.000000002297 0.57302 3.25
10 4B1V LAB 0.00000005116 0.57265 3.25
11 1SQK ADP 0.000000004599 0.52737 3.25
12 4Z94 ATP 0.00000003782 0.51184 3.25
13 4B1X LAB 0.0003453 0.50714 3.25
14 4RW3 PLM 0.01634 0.42928 3.31126
15 4RW3 SHV 0.009886 0.41479 3.31126
16 3AAQ ARU 0.0001057 0.46577 3.39943
17 2YCH ATP 0.000000005102 0.66769 3.44828
18 1KXP ATP 0.000000002067 0.70153 3.46667
19 2FXU ATP 0.00000008231 0.61668 3.46667
20 3SJH ATP 0.000000002447 0.57212 3.46667
21 3SJH LAR 0.0000000743 0.56949 3.46667
22 4H03 ATP 0.0000001024 0.5615 3.46667
23 4H03 LAR 0.0000001162 0.55124 3.46667
24 4A59 AMP 0.004269 0.42201 3.5
25 2E2P ADP 0.002997 0.44444 3.67893
26 2ZGY GDP 0.0000001452 0.62731 3.75
27 4PKG ATP 0.000000003326 0.69239 3.76344
28 2FF3 ATP 0.000000001901 0.56538 4
29 2FF6 ATP 0.000000002408 0.5608 4
30 4MO4 ACP 0.0001358 0.46419 4.04313
31 1T44 ATP 0.000000003482 0.55643 4.08163
32 4A2B AGS 0.0000002032 0.51464 4.25
33 4A2A ATP 0.0000002571 0.50534 4.25
34 2A42 ATP 0.000000002542 0.56225 4.61538
35 2A3Z ATP 0.000000002999 0.56057 4.61538
36 2A40 ATP 0.000000002921 0.56007 4.61538
37 3CIP ATP 0.00000003755 0.50345 4.8
38 3BF1 ADP 0.0002526 0.41434 4.81928
39 4BGB ADP 0.0004061 0.49739 4.92308
40 2YVK MRU 0.01404 0.40521 5.08021
41 3U4L ATP 0.000000001406 0.58019 5.33333
42 3MN6 ATP 0.000000001264 0.70204 5.34759
43 3MN9 ATP 0.000000004771 0.55433 5.34759
44 4PL8 ATP 0.000000003305 0.69251 5.47945
45 5HTX ADP 0.0002704 0.5063 5.5
46 3WMX THR 0.01604 0.40858 5.58659
47 1YAG ATP 0.0000000002873 0.62109 5.86667
48 4B1W ATP 0.0000000004869 0.60313 6.25
49 3G6N MET ALA SER 0.03161 0.40942 6.28272
50 4YDU ADP 0.00006071 0.43638 6.32911
51 5FS0 5JC 0.03829 0.40105 6.63507
52 4EHU ANP 0.0000001578 0.53043 6.88406
53 2Q97 ATP 0.00009332 0.48111 6.97674
54 4CBU ATP 0.000000002215 0.6674 7.08661
55 2G2Y MLI 0.03601 0.40258 7.14286
56 5EOU ATP 0.000000006474 0.56026 7.52688
57 3MAN BMA BMA MAN 0.03519 0.4054 7.94702
58 3MN7 ATP 0.0000000006253 0.59904 8.16327
59 4FE2 ADP 0.02346 0.40465 8.23529
60 3WQT ANP 0.00000001068 0.55487 9.25
61 4PKI ATP 0.000000002511 0.5618 10.1852
62 3U9Z ADP 0.00000000254 0.71618 10.3448
63 2PAV ATP 0.00000003972 0.58568 10.7914
64 2PBD ATP 0.000000001581 0.56697 10.7914
65 4CBX ATP 0.000000001747 0.70476 11.3757
66 4BR5 ANP 0.0002628 0.4464 11.75
67 4ZLU ADP 0.000036 0.48089 13
68 4ZLU 4PW 0.000036 0.48089 13
69 2IVN ANP 0.00002983 0.49359 13.0303
70 1YRO UDP 0.02615 0.41053 13.2867
71 5LJW ANP 0.000000008588 0.52124 14.121
72 2ZFZ ARG 0.03147 0.40338 18.9873
73 4CZG ADP 0.000000001668 0.64698 19.2529
74 4CZG QH3 0.000000001903 0.64698 19.2529
75 4EFH ADP 0.000000001347 0.55112 21.2121
76 2D0O ADP 0.0000003304 0.63498 21.75
77 1QKQ MAN 0.001482 0.43503 24.6479
78 4B1Y ATP 0.000000004574 0.57063 28.125
79 3MN5 ATP 0.000000002878 0.56976 34.2105
80 2V52 ATP 0.000000002052 0.57524 34.375
81 2D1K ATP 0.000000003148 0.55963 34.375
82 4A62 ANP 0.0000005018 0.58285 35.2941
83 5LY3 ADP 0.00000008736 0.63727 43.75
Pocket No.: 2; Query (leader) PDB : 5F1X; Ligand: ATP; Similar sites found: 13
This union binding pocket(no: 2) in the query (biounit: 5f1x.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1U1J MET 0.02998 0.40303 2
2 4OEV OXL 0.01917 0.42295 2.5
3 2AOU CQA 0.02247 0.41319 3.42466
4 2AUY NAG MAN MMA 0.01465 0.41114 3.57143
5 2GND MAN 0.04079 0.40366 3.57143
6 1Q8Q MAN MMA 0.04279 0.40249 3.57143
7 1Q9I FAD 0.01345 0.40026 3.85289
8 1Q9I TEO 0.01345 0.40026 3.85289
9 2QV7 ADP 0.01774 0.40371 7.12166
10 4OAS 2SW 0.01825 0.40651 7.29167
11 2JHP GUN 0.04535 0.40793 7.5
12 4FHT DHB 0.03025 0.41231 8.28025
13 4LWU 20U 0.01355 0.41278 9.41177
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