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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 with APoc: 104
This union binding pocket(no: 1) in the query (biounit: 5bv3.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 4CQK PIO None
2 5KK4 44E None
3 5C9P FUC 1.73913
4 5AWM ANP 1.73913
5 1OS7 TAU 1.76678
6 5VLQ ANP 2.02899
7 6EOM ALA LYS 2.02899
8 6F7X MFU 2.22222
9 4N14 WR7 2.2293
10 5WSY 7UC 2.31214
11 6C1S EFV 2.31884
12 4Y8D 49J 2.35294
13 1S68 AMP 2.40964
14 2GWH PCI 2.68456
15 4ZNO SUC 2.68657
16 4DFU QUE 2.79503
17 5OES ADP 2.89855
18 3GDN MXN 2.89855
19 4ZXA H8N 2.97619
20 4JSR 1NQ 3.15789
21 4D4U FUC GAL NAG 3.1746
22 3HDY FDA 3.18841
23 3HDY GDU 3.18841
24 3HDY FAD 3.18841
25 3R4S SIA 3.18841
26 5C1P ADP 3.26797
27 5UMW RBF 3.31126
28 3ZW2 NAG GAL FUC 3.44828
29 3ZW0 FUC 3.44828
30 2IF8 ADP 3.47826
31 5WS9 ATP 3.47826
32 3QDY A2G GAL 3.4965
33 3QDW A2G 3.4965
34 3QDX A2G GAL 3.4965
35 3HAV ATP 3.67893
36 4CS9 AMP 3.7037
37 4OX5 DAL 3.74332
38 3VSV XYS 3.76812
39 5AVF TAU 3.89105
40 4JGT PYR 4.01338
41 4R78 AMP 4.20712
42 2XOC ADP 4.21456
43 4PZ6 GMP 4.34783
44 1V2F HCI 4.34783
45 3SAO NKN 4.375
46 4CSD MFU 4.41176
47 5HVJ ANP 4.44444
48 1OFZ FUL 4.48718
49 1OFZ FUC 4.48718
50 3X01 AMP 4.63768
51 1O9U ADZ 4.63768
52 6AC9 ANP 4.63768
53 1PK8 ATP 4.63768
54 1TZD ADP 4.72727
55 1UPR 4IP 4.87805
56 1W2D ADP 4.90566
57 2VGD XYP XYP 5.04587
58 5GVL GI8 5.21739
59 5GVL PLG 5.21739
60 5FIT AP2 5.44218
61 5VZ0 ADP 5.50725
62 2TPS TPS 5.72687
63 5L6G XYP 5.7971
64 4MJ0 SIA SIA 5.81818
65 6E8I PTR 5.91716
66 4YMJ 4EJ 5.92105
67 2Q4H AMP 6.08696
68 2V58 LZJ 6.08696
69 4INI AMP 6.15385
70 5WA9 9ZD 6.20155
71 4NFE BEN 6.32911
72 1AV5 AP2 6.34921
73 3VOT ADP 6.37681
74 4P7X AKG 6.50685
75 4P7X YCP 6.50685
76 4U0I 0LI 6.66667
77 5OKT 9XK 6.6879
78 1GU3 BGC BGC BGC BGC BGC 6.71141
79 3N1S 5GP 6.72269
80 5RHN 8BR 6.95652
81 5OFW 9TW 7.17489
82 3EM0 CHD 7.24638
83 1C5C TK4 7.47664
84 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU 7.89474
85 1NU4 MLA 8.24742
86 5F90 GLA GAL 8.33333
87 5F90 GLA GAL BGC 5VQ 8.33333
88 4BHN BH9 8.38323
89 4TVD GLC 8.4058
90 2WW4 ADP 8.48057
91 1M0W ANP 8.69565
92 3BP1 GUN 8.96552
93 3FSY SCA 9.03614
94 4PTN PYR 9.0379
95 4AG8 AXI 11.0759
96 2CST MAE 12.1739
97 3PUR 2HG 13.0435
98 2BS5 BGC GAL FUC 13.3333
99 3ANY 2A3 14.8289
100 4XBA 5GP 16
101 4XBA GMP 16
102 3LQV ADE 16.5217
103 1RGE 2GP 23.9583
104 1ST0 GTG 48.6647
Pocket No.: 2; Query (leader) PDB : 5BV3; Ligand: M7G; Similar sites found with APoc: 15
This union binding pocket(no: 2) in the query (biounit: 5bv3.bio2) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 2H8Z 8CM 1.15942
2 3UYW TAU 1.86916
3 1ZX5 LFR 2
4 3ZW2 GLA NAG GAL FUC 3.44828
5 5Y4R C2E 4.82759
6 1J3R 6PG 5.26316
7 5V8E CIT 6.14887
8 2P7Q GG6 6.76692
9 3MYZ TFX 7
10 4B5W PYR 7.42188
11 1AUX AGS 7.71704
12 5N53 8NB 8.20513
13 2QX0 PH2 10.0629
14 5A9A UTP 10.2881
15 3DGY 2GP 11.3402
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