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Receptor
PDB id Resolution Class Description Source Keywords
1XMM 2.5 Å EC: 3.-.-.- STRUCTURE OF HUMAN DCPS BOUND TO M7GDP HOMO SAPIENS SCAVENGER DECAPPING ENZYME BOUND M7GDP CHAPERONE
Ref.: CRYSTAL STRUCTURES OF HUMAN DCPS IN LIGAND-FREE AND M7GDP-BOUND FORMS SUGGEST A DYNAMIC MECHANISM FOR S MRNA DECAPPING. J.MOL.BIOL. V. 347 707 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
G7M B:1502;
C:503;
Valid;
Valid;
none;
none;
submit data
378.255 C11 H17 N5 O8 P C[n+]...
M7G A:401;
D:404;
Valid;
Valid;
none;
none;
submit data
459.243 C11 H19 N5 O11 P2 CN1CN...
PO4 A:1601;
B:602;
C:603;
D:1604;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1ST0 1.9 Å EC: 3.-.-.- STRUCTURE OF DCPS BOUND TO M7GPPPG HOMO SAPIENS RNA DECAY EXOSOME DECAPPING HIT PROTEIN MESSENGER RNA MRNA CAP RNA BINDING PROTEIN
Ref.: INSIGHTS INTO THE STRUCTURE, MECHANISM, AND REGULATION OF SCAVENGER MRNA DECAPPING ACTIVITY MOL.CELL V. 14 67 2004
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 253 families.
1 1XMM - M7G C11 H19 N5 O11 P2 CN1CN(C2=C....
2 1ST4 - GTA C21 H30 N10 O17 P3 C[n+]1cn(c....
3 1ST0 - GTG C21 H30 N10 O18 P3 C[n+]1cn(c....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 209 families.
1 3BL9 ic50 = 43.94 nM DD2 C21 H23 Cl2 N5 O c1cc(c(c(c....
2 3BL7 ic50 = 7.62 nM DD1 C21 H24 F N5 O c1ccc(c(c1....
3 5OSY ic50 = 0.0447 uM AJQ C21 H30 N10 O15 P3 S3 C[n+]1cn(c....
4 1XMM - M7G C11 H19 N5 O11 P2 CN1CN(C2=C....
5 1ST4 - GTA C21 H30 N10 O17 P3 C[n+]1cn(c....
6 1ST0 - GTG C21 H30 N10 O18 P3 C[n+]1cn(c....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 173 families.
1 3BL9 ic50 = 43.94 nM DD2 C21 H23 Cl2 N5 O c1cc(c(c(c....
2 3BL7 ic50 = 7.62 nM DD1 C21 H24 F N5 O c1ccc(c(c1....
3 5OSY ic50 = 0.0447 uM AJQ C21 H30 N10 O15 P3 S3 C[n+]1cn(c....
4 1XMM - M7G C11 H19 N5 O11 P2 CN1CN(C2=C....
5 1ST4 - GTA C21 H30 N10 O17 P3 C[n+]1cn(c....
6 1ST0 - GTG C21 H30 N10 O18 P3 C[n+]1cn(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: G7M; Similar ligands found: 65
No: Ligand ECFP6 Tc MDL keys Tc
1 G7M 1 1
2 MGP 0.794872 0.987013
3 6G0 0.78481 0.987013
4 MG7 0.728571 0.871795
5 GTG 0.655914 0.962025
6 GTA 0.652632 0.962025
7 MGQ 0.629214 0.936709
8 GDP 7MG 0.625 0.961538
9 MGV 0.608696 0.891566
10 5GP 0.583333 0.960526
11 G 0.583333 0.960526
12 AJQ 0.5 0.914634
13 GDP 0.483871 0.948052
14 AIR 0.481013 0.855263
15 GP3 0.473118 0.924051
16 MGO 0.46875 0.888889
17 GTP 0.46875 0.948052
18 GP2 0.468085 0.9125
19 GNH 0.463158 0.935897
20 G2P 0.459184 0.9125
21 GMV 0.453608 0.924051
22 A 0.453488 0.87013
23 AMP 0.453488 0.87013
24 C2R 0.452381 0.858974
25 AMZ 0.452381 0.87013
26 93A 0.450549 0.793103
27 GAV 0.45 0.9125
28 XMP 0.449438 0.897436
29 GCP 0.44898 0.924051
30 G1R 0.44898 0.935897
31 GSP 0.444444 0.901235
32 9GM 0.444444 0.924051
33 GNP 0.444444 0.924051
34 NIA 0.44186 0.829268
35 IMP 0.43956 0.934211
36 ALF 5GP 0.438776 0.890244
37 RMB 0.438202 0.805195
38 GPG 0.432692 0.9125
39 RBZ 0.431818 0.807692
40 Y9Z 0.429907 0.880952
41 71V 0.428571 0.819277
42 PMO 0.428571 0.807692
43 G2R 0.423077 0.9125
44 AAM 0.422222 0.87013
45 7RA 0.422222 0.883117
46 IMO 0.422222 0.833333
47 YGP 0.420561 0.902439
48 1RB 0.420455 0.792208
49 GDC 0.416667 0.9125
50 GKE 0.416667 0.9125
51 GDD 0.416667 0.9125
52 GDP AF3 0.413462 0.890244
53 ALF GDP 0.413462 0.890244
54 GDP ALF 0.413462 0.890244
55 GDR 0.412844 0.936709
56 GFB 0.412844 0.936709
57 IRN 0.4125 0.776316
58 G3A 0.409091 0.924051
59 FAI 0.406593 0.87013
60 G5P 0.405405 0.924051
61 GKD 0.401786 0.9125
62 JB2 0.401786 0.936709
63 NGD 0.401709 0.936709
64 5O8 0.4 0.729167
65 G G 0.4 0.948718
Ligand no: 2; 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 : 1ST0; Ligand: GTG; Similar sites found with APoc: 125
This union binding pocket(no: 1) in the query (biounit: 1st0.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
1 5XG5 A2G None
2 4CQK PIO None
3 2VGD XYP XYP 0.917431
4 2ZQO NGA 1.53846
5 4YLZ LAT NAG GAL 1.96078
6 3BP1 GUN 2.06897
7 3DJE FSA 2.07715
8 3WDX BGC BGC GLC 2.34899
9 2Q4H AMP 2.37389
10 2ZBL BMA 2.37389
11 2WW4 ADP 2.4735
12 4G05 JZ3 2.52366
13 4NFE BEN 2.53165
14 5OKT 9XK 2.54777
15 5OFW 9TW 2.69058
16 1J84 BGC BGC BGC BGC 2.77778
17 4EE7 PIS 2.96053
18 1Z03 OCH 2.96736
19 3PD6 KYN 2.96736
20 3PDB OAA 2.96736
21 2PUL ACP 2.96736
22 1W2D ADP 3.01887
23 5N53 8NB 3.07692
24 5MUA GAL 3.14685
25 6AC9 ANP 3.2641
26 3HAV ATP 3.34448
27 3WV6 GAL GLC 3.37838
28 3WV6 GAL BGC 3.37838
29 3G4Q MCH 3.42466
30 4MZU TYD 3.52564
31 5OES ADP 3.56083
32 3PUR 2HG 3.56083
33 3WUD GLC GAL 3.67647
34 1SLT NDG GAL 3.73134
35 3QRC SCR 3.82166
36 1JPA ANP 3.84615
37 3GDN MXN 3.85757
38 2AY3 MPP 3.85757
39 5W1E PHB 3.85757
40 1UMZ BGC BGC XYS BGC XYS GAL 3.95683
41 5KTI TRE 6X6 4.02685
42 3KDM TES 4.12844
43 1O9U ADZ 4.1543
44 1V2F HCI 4.1543
45 5GLT BGC GAL NAG GAL 4.22535
46 4FGC PQ0 4.24242
47 5NLD LBT 4.31655
48 4BTV RB3 4.36047
49 1S68 AMP 4.41767
50 1LSH PLD 4.45104
51 6EOM ALA LYS 4.45104
52 2YBP 2HG 4.45104
53 1Y7P RIP 4.4843
54 3ZW2 NAG GAL FUC 4.5977
55 6GR0 F8W 4.5977
56 6E8I PTR 4.73373
57 1M0W ANP 4.74777
58 1EU1 GLC 4.74777
59 2YIV NBN 4.74777
60 4OPC FDA 4.74777
61 5EO8 TFU 4.82315
62 5F90 GLA GAL 5.12821
63 5F90 GLA GAL BGC 5VQ 5.12821
64 6D61 4AA 5.12821
65 2HZQ STR 5.17241
66 6GNO XDI 5.18518
67 3OYW TDG 5.22388
68 1ULE GLA GAL NAG 5.33333
69 5VLQ ANP 5.34125
70 4ZXA H8N 5.35714
71 5LNE A2G GAL 5.4878
72 2OFD NGA 5.6338
73 4HSJ 6PC 5.74713
74 2IF8 ADP 5.78512
75 2Z48 NGA 5.93472
76 2QCD U5P 6.15385
77 4WVW SLT 6.25
78 1KJ1 MAN 6.42202
79 6A63 LAT 6.52174
80 1A78 TDG 6.71642
81 1O4T OXL 6.76692
82 5VZ0 ADP 6.82493
83 3QDW A2G 6.99301
84 1YAA MAE 7.12166
85 3NV3 GAL NAG MAN 7.24638
86 4K55 H6P 7.25806
87 1GU3 BGC BGC BGC BGC BGC 7.38255
88 1XF1 CIT 7.71513
89 5JSP DQY 8.01187
90 2QL9 CIT 8.09249
91 5C1P ADP 8.16993
92 3VV1 GAL FUC 8.75
93 1WW5 SGA BGC 8.75
94 2XOC ADP 8.81226
95 1IS3 LAT 8.88889
96 2BS5 BGC GAL FUC 8.88889
97 5T7I LAT NAG GAL 9.03226
98 2YMZ LAT 9.23077
99 3KFF ZBT 9.25926
100 3KFF XBT 9.25926
101 3M3E GAL A2G NPO 9.31677
102 5DG2 GAL GLC 9.62963
103 4JGP PYR 9.67742
104 3SAO DBH 10
105 4QXB OGA 10.2941
106 2XOM GAL GAL GAL 10.5263
107 5C79 PBU 10.6667
108 1YQC GLV 10.6825
109 5FIT AP2 10.8844
110 4XBA 5GP 11.5
111 4XBA GMP 11.5
112 4LIT AKG 11.5727
113 2CST MAE 12.4629
114 3VSV XYS 12.4629
115 3N1S 5GP 12.605
116 3ZXE PGZ 12.782
117 5NFB 8VT 13.0682
118 2D6M LBT 13.2075
119 1NU4 MLA 13.4021
120 5H9P TD2 14.557
121 1UPR 4IP 14.6341
122 1DZT TPE 15.3005
123 4CS9 AMP 15.873
124 3LQV ADE 25.641
125 5BV3 M7G 48.6647
Pocket No.: 2; Query (leader) PDB : 1ST0; Ligand: GTG; Similar sites found with APoc: 31
This union binding pocket(no: 2) in the query (biounit: 1st0.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 5KK4 44E None
2 6F7X MFU None
3 2Q09 DI6 1.18694
4 4LH7 1X8 1.54799
5 3OBT SLB 2.07715
6 1ZX5 LFR 2.33333
7 3FSY SCA 2.40964
8 2I74 MAN MAN MAN MAN 2.6455
9 3X01 AMP 2.67062
10 4CC6 L5Y 2.83019
11 1TMX BEZ 3.07167
12 1OS7 TAU 3.18021
13 4PZ6 GMP 3.2641
14 2QX0 PH2 3.77358
15 3W6X HZP 3.93013
16 1TZD ADP 4
17 4CM9 YGL 4.16667
18 2TPS TPS 4.40529
19 5HVJ ANP 4.44444
20 4ZGR NGA GAL 4.5977
21 5F90 LMR 5.12821
22 4CSD MFU 5.14706
23 3NX2 FER 5.35714
24 2Z49 AMG 5.93472
25 2Z48 A2G 5.93472
26 5L4R CPT 6.76329
27 3QDV A2G 6.99301
28 1QPR PHT 9.15493
29 3PN1 IVH 10.3774
30 4PTN PYR 11.276
31 1SQL GUN 19.1781
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