Receptor
PDB id Resolution Class Description Source Keywords
5BV3 2.25 Å EC: 3.6.1.59 YEAST SCAVENGER DECAPPING ENZYME IN COMPLEX WITH M7GDP SACCHAROMYCES CEREVISIAE (STRAIN ATCC S288C) SCAVENGER DECAPPING ENZYME CAP STRUCTURE DECAPPING ENZYMESUBSTRATE INHIBITION PROTEIN DYNAMICS HYDROLASE
Ref.: AN EXCESS OF CATALYTICALLY REQUIRED MOTIONS INHIBIT SCAVENGER DECAPPING ENZYME. NAT.CHEM.BIOL. V. 11 697 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL C:403;
D:404;
D:403;
A:404;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
35.453 Cl [Cl-]
SO4 B:401;
A:403;
A:402;
D:402;
B:402;
D:401;
C:402;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
M7G C:401;
A:401;
Valid;
Valid;
none;
none;
Kd = 196 uM
459.243 C11 H19 N5 O11 P2 CN1CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5BV3 2.25 Å EC: 3.6.1.59 YEAST SCAVENGER DECAPPING ENZYME IN COMPLEX WITH M7GDP SACCHAROMYCES CEREVISIAE (STRAIN ATCC S288C) SCAVENGER DECAPPING ENZYME CAP STRUCTURE DECAPPING ENZYMESUBSTRATE INHIBITION PROTEIN DYNAMICS HYDROLASE
Ref.: AN EXCESS OF CATALYTICALLY REQUIRED MOTIONS INHIBIT SCAVENGER DECAPPING ENZYME. NAT.CHEM.BIOL. V. 11 697 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5BV3 Kd = 196 uM M7G C11 H19 N5 O11 P2 CN1CN(C2=C....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5BV3 Kd = 196 uM M7G C11 H19 N5 O11 P2 CN1CN(C2=C....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5BV3 Kd = 196 uM M7G C11 H19 N5 O11 P2 CN1CN(C2=C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: M7G; Similar ligands found: 11
No: Ligand ECFP6 Tc MDL keys Tc
1 M7G 1 1
2 MGT 0.910256 1
3 M7M 0.541667 0.963855
4 G8D 0.537634 0.914634
5 TPG 0.525 0.920455
6 8GT 0.494845 0.914634
7 CDP 0.43617 0.829268
8 UDP 0.430108 0.780488
9 8GM 0.412371 0.902439
10 8OD 0.411765 0.77907
11 8GD 0.407767 0.872093
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5BV3; Ligand: M7G; Similar sites found: 58
This union binding pocket(no: 1) in the query (biounit: 5bv3.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4CQK PIO 0.01219 0.4176 None
2 5AWM ANP 0.007279 0.41854 1.73913
3 4N14 WR7 0.00583 0.43421 2.2293
4 5WSY 7UC 0.02116 0.40002 2.31214
5 4Y8D 49J 0.01506 0.41182 2.35294
6 4AZT LY2 0.001831 0.44748 2.6087
7 4DFU QUE 0.02516 0.4004 2.79503
8 4ZXA H8N 0.01397 0.40901 2.97619
9 4D4U FUC GAL NAG 0.02117 0.40001 3.1746
10 3R4S SIA 0.01697 0.40164 3.18841
11 5C1P ADP 0.01349 0.40162 3.26797
12 5DA3 58V 0.01284 0.40661 3.39623
13 3ZW0 FUC 0.006634 0.43158 3.44828
14 2IF8 ADP 0.008089 0.4256 3.47826
15 3HAV ATP 0.009957 0.42427 3.67893
16 4CS9 AMP 0.004527 0.43944 3.7037
17 4OX5 DAL 0.02585 0.40611 3.74332
18 3VSV XYS 0.01417 0.41488 3.76812
19 5AVF TAU 0.009839 0.41659 3.89105
20 4JGT PYR 0.01237 0.42355 4.01338
21 4R78 AMP 0.007372 0.42281 4.20712
22 3SAO NKN 0.009871 0.41214 4.375
23 4CSD MFU 0.007648 0.4282 4.41176
24 5HVJ ANP 0.01071 0.42402 4.44444
25 1OFZ FUL 0.004279 0.44292 4.48718
26 1OFZ FUC 0.0207 0.40603 4.48718
27 3X01 AMP 0.0009016 0.47803 4.63768
28 1TZD ADP 0.02252 0.40855 4.72727
29 1UPR 4IP 0.01638 0.41402 4.87805
30 1W2D ADP 0.005509 0.42439 4.90566
31 2VGD XYP XYP 0.01488 0.41189 5.04587
32 5VZ0 ADP 0.003156 0.42278 5.50725
33 5L6G XYP 0.009926 0.42021 5.7971
34 4MJ0 SIA SIA 0.02336 0.4049 5.81818
35 4YMJ 4EJ 0.01726 0.41038 5.92105
36 2Q4H AMP 0.00004415 0.44437 6.08696
37 4INI AMP 0.000004583 0.55724 6.15385
38 5I2E 67D 0.00003912 0.53734 6.20155
39 1AV5 AP2 0.00001124 0.54648 6.34921
40 3VOT ADP 0.01293 0.40646 6.37681
41 4P7X AKG 0.006443 0.40519 6.50685
42 4P7X YCP 0.006443 0.40519 6.50685
43 3N1S 5GP 0.000003401 0.57089 6.72269
44 5OFW 9TW 0.02328 0.40221 7.17489
45 5F90 GLA GAL 0.006275 0.43098 8.33333
46 5F90 GLA GAL BGC 5VQ 0.02145 0.40265 8.33333
47 4TVD GLC 0.004281 0.41851 8.4058
48 2WW4 ADP 0.01202 0.404 8.48057
49 3BP1 GUN 0.007795 0.43471 8.96552
50 4PTN PYR 0.006851 0.44096 9.0379
51 2CST MAE 0.01115 0.41848 12.1739
52 3PUR 2HG 0.01684 0.41087 13.0435
53 3ANY 2A3 0.004325 0.43472 14.8289
54 4XBA 5GP 0.00000331 0.56373 16
55 4XBA GMP 0.000007542 0.55463 16
56 3LQV ADE 0.003427 0.44798 16.5217
57 1RGE 2GP 0.01895 0.40873 23.9583
58 1ST0 GTG 0.0000000000002427 0.63373 48.6647
Pocket No.: 2; Query (leader) PDB : 5BV3; Ligand: M7G; Similar sites found: 5
This union binding pocket(no: 2) in the query (biounit: 5bv3.bio2) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3UYW TAU 0.04334 0.40321 1.86916
2 1ZX5 LFR 0.04411 0.40046 2
3 3MYZ TFX 0.02768 0.44007 7
4 5N53 8NB 0.02791 0.401 8.20513
5 3DGY 2GP 0.03007 0.40058 11.3402
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