Receptor
PDB id Resolution Class Description Source Keywords
2GSP 1.8 Å EC: 3.1.27.3 RIBONUCLEASE T1/2',3'-CGPS AND 3'-GMP, 2 DAYS ASPERGILLUS ORYZAE HYDROLASE ENDORIBONUCLEASE
Ref.: HYDROLYSIS OF A SLOW CYCLIC THIOPHOSPHATE SUBSTRATE T1 ANALYZED BY TIME-RESOLVED CRYSTALLOGRAPHY. NAT.STRUCT.BIOL. V. 5 280 1998
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3GP A:106;
Valid;
none;
submit data
363.221 C10 H14 N5 O8 P c1nc2...
CA A:107;
Part of Protein;
none;
submit data
40.078 Ca [Ca+2...
SGP A:105;
Valid;
none;
submit data
361.271 C10 H12 N5 O6 P S c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1RNT 1.9 Å EC: 3.1.27.3 RESTRAINED LEAST-SQUARES REFINEMENT OF THE CRYSTAL STRUCTURE RIBONUCLEASE T1(ASTERISK)2(PRIME)-GUANYLIC ACID COMPLEX AT A NGSTROMS RESOLUTION ASPERGILLUS ORYZAE HYDROLASE(ENDORIBONUCLEASE)
Ref.: RESTRAINED LEAST-SQUARES REFINEMENT OF THE CRYSTAL OF THE RIBONUCLEASE T1(ASTERISK)2(PRIME)-GUANYLIC A COMPLEX AT 1.9 ANGSTROMS RESOLUTION ACTA CRYSTALLOGR.,SECT.B V. 43 548 1987
Members (54)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 6GSP - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
2 1TRP - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
3 5GSP - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
4 7RNT - 2AM C10 H14 N5 O7 P c1nc(c2c(n....
5 1FYS - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
6 1LOV - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
7 6RNT Kd = 4.3 mM 2AM C10 H14 N5 O7 P c1nc(c2c(n....
8 1RGA - G C10 H14 N5 O8 P c1nc2c(n1[....
9 1RLS - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
10 1LOW - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
11 1I2F - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
12 1DET Kd = 50 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
13 1HZ1 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
14 5BIR Kd = 255 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
15 1FZU - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
16 1B2M - G U34 n/a n/a
17 1BVI - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
18 1I2E - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
19 1G02 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
20 1BIR Kd = 138 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
21 1RNT Kd = 6.5 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
22 3BIR Kd = 112 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
23 1CH0 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
24 1I3I - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
25 4GSP - SGP C10 H12 N5 O6 P S c1nc2c(n1[....
26 2AAD - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
27 5HOH - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
28 3BU4 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
29 3SYU Kd = 50 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
30 1I0V - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
31 1RHL - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
32 1I2G - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
33 1I0X - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
34 1RGK Kd = 49 uM 2AM C10 H14 N5 O7 P c1nc(c2c(n....
35 1I3F - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
36 1LRA - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
37 4HOH - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
38 2RNT - GPG C20 H25 N10 O12 P c1nc2c(n1[....
39 2BU4 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
40 5BU4 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
41 2BIR - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
42 1RGC - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
43 1GSP - SGP C10 H12 N5 O6 P S c1nc2c(n1[....
44 2HOH - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
45 1HYF - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
46 7GSP - SGP C10 H12 N5 O6 P S c1nc2c(n1[....
47 3GSP - SGP C10 H12 N5 O6 P S c1nc2c(n1[....
48 3HOH - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
49 1LOY - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
50 1BU4 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
51 2GSP - SGP C10 H12 N5 O6 P S c1nc2c(n1[....
52 1RGL Kd = 37 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
53 1TRQ - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
54 4BU4 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
70% Homology Family (57)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 6GSP - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
2 1TRP - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
3 5GSP - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
4 7RNT - 2AM C10 H14 N5 O7 P c1nc(c2c(n....
5 1FYS - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
6 1LOV - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
7 6RNT Kd = 4.3 mM 2AM C10 H14 N5 O7 P c1nc(c2c(n....
8 1RGA - G C10 H14 N5 O8 P c1nc2c(n1[....
9 1RLS - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
10 1LOW - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
11 1I2F - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
12 1DET Kd = 50 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
13 1HZ1 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
14 5BIR Kd = 255 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
15 1FZU - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
16 1B2M - G U34 n/a n/a
17 1BVI - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
18 1I2E - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
19 1G02 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
20 1BIR Kd = 138 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
21 1RNT Kd = 6.5 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
22 3BIR Kd = 112 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
23 1CH0 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
24 1I3I - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
25 4GSP - SGP C10 H12 N5 O6 P S c1nc2c(n1[....
26 2AAD - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
27 5HOH - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
28 3BU4 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
29 3SYU Kd = 50 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
30 1I0V - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
31 1RHL - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
32 1I2G - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
33 1I0X - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
34 1RGK Kd = 49 uM 2AM C10 H14 N5 O7 P c1nc(c2c(n....
35 1I3F - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
36 1LRA - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
37 4HOH - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
38 2RNT - GPG C20 H25 N10 O12 P c1nc2c(n1[....
39 2BU4 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
40 5BU4 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
41 2BIR - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
42 1RGC - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
43 1GSP - SGP C10 H12 N5 O6 P S c1nc2c(n1[....
44 2HOH - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
45 1HYF - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
46 7GSP - SGP C10 H12 N5 O6 P S c1nc2c(n1[....
47 3GSP - SGP C10 H12 N5 O6 P S c1nc2c(n1[....
48 3HOH - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
49 1LOY - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
50 1BU4 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
51 2GSP - SGP C10 H12 N5 O6 P S c1nc2c(n1[....
52 1RGL Kd = 37 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
53 1TRQ - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
54 4BU4 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
55 1RMS - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
56 1RDS - GPC C19 H24 F N8 O11 P c1nc2c(n1[....
57 1FUT - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
50% Homology Family (60)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 6GSP - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
2 1TRP - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
3 5GSP - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
4 7RNT - 2AM C10 H14 N5 O7 P c1nc(c2c(n....
5 1FYS - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
6 1LOV - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
7 6RNT Kd = 4.3 mM 2AM C10 H14 N5 O7 P c1nc(c2c(n....
8 1RGA - G C10 H14 N5 O8 P c1nc2c(n1[....
9 1RLS - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
10 1LOW - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
11 1I2F - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
12 1DET Kd = 50 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
13 1HZ1 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
14 5BIR Kd = 255 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
15 1FZU - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
16 1B2M - G U34 n/a n/a
17 1BVI - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
18 1I2E - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
19 1G02 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
20 1BIR Kd = 138 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
21 1RNT Kd = 6.5 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
22 3BIR Kd = 112 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
23 1CH0 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
24 1I3I - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
25 4GSP - SGP C10 H12 N5 O6 P S c1nc2c(n1[....
26 2AAD - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
27 5HOH - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
28 3BU4 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
29 3SYU Kd = 50 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
30 1I0V - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
31 1RHL - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
32 1I2G - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
33 1I0X - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
34 1RGK Kd = 49 uM 2AM C10 H14 N5 O7 P c1nc(c2c(n....
35 1I3F - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
36 1LRA - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
37 4HOH - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
38 2RNT - GPG C20 H25 N10 O12 P c1nc2c(n1[....
39 2BU4 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
40 5BU4 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
41 2BIR - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
42 1RGC - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
43 1GSP - SGP C10 H12 N5 O6 P S c1nc2c(n1[....
44 2HOH - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
45 1HYF - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
46 7GSP - SGP C10 H12 N5 O6 P S c1nc2c(n1[....
47 3GSP - SGP C10 H12 N5 O6 P S c1nc2c(n1[....
48 3HOH - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
49 1LOY - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
50 1BU4 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
51 2GSP - SGP C10 H12 N5 O6 P S c1nc2c(n1[....
52 1RGL Kd = 37 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
53 1TRQ - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
54 4BU4 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
55 1RMS - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
56 1RDS - GPC C19 H24 F N8 O11 P c1nc2c(n1[....
57 3AGO - 3AM C10 H14 N5 O7 P c1nc(c2c(n....
58 3AHW - 2AM C10 H14 N5 O7 P c1nc(c2c(n....
59 3AGN - 3AM C10 H14 N5 O7 P c1nc(c2c(n....
60 1FUT - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 3GP; Similar ligands found: 105
No: Ligand ECFP6 Tc MDL keys Tc
1 3GP 1 1
2 G3D 0.753086 0.959459
3 2GP 0.733333 0.959459
4 GMP 0.704225 0.853333
5 G4P 0.674419 0.959459
6 G 0.65 0.959459
7 5GP 0.65 0.959459
8 0O2 0.644444 0.959459
9 GDP 0.611765 0.946667
10 GNH 0.604651 0.934211
11 GCP G 0.602151 0.945946
12 GP3 0.6 0.922078
13 GSP 0.595506 0.898734
14 GP2 0.593023 0.910256
15 GPG 0.591398 0.935065
16 GTP 0.590909 0.946667
17 G2P 0.577778 0.910256
18 G G 0.57732 0.922078
19 G U34 0.576923 0.8875
20 G U 0.576923 0.898734
21 GMV 0.573034 0.922078
22 ALF 5GP 0.573034 0.864198
23 P2G 0.571429 0.932432
24 GDC 0.56701 0.935065
25 GKE 0.56701 0.935065
26 GDD 0.56701 0.935065
27 G1R 0.566667 0.934211
28 GCP 0.566667 0.922078
29 G C 0.566038 0.898734
30 GAV 0.565217 0.910256
31 G A A A 0.560748 0.922078
32 GNP 0.56044 0.922078
33 9GM 0.56044 0.922078
34 P1G 0.55814 0.92
35 GDP ALF 0.536842 0.864198
36 GDP AF3 0.536842 0.864198
37 ALF GDP 0.536842 0.864198
38 KB7 0.533333 0.825
39 G2R 0.53125 0.910256
40 KBD 0.525773 0.825
41 A G 0.518182 0.909091
42 SGP 0.517241 0.871795
43 GDR 0.514852 0.910256
44 GFB 0.514852 0.910256
45 GKD 0.514563 0.935065
46 U A G G 0.513514 0.909091
47 YGP 0.51 0.876543
48 6CK 0.509804 0.8875
49 G3A 0.509804 0.922078
50 U2G 0.509259 0.911392
51 BGO 0.509259 0.898734
52 G G G RPC 0.509091 0.897436
53 DG 0.505747 0.909091
54 DGP 0.505747 0.909091
55 GH3 0.505263 0.946667
56 KBJ 0.504951 0.795181
57 Y9Z 0.504951 0.878049
58 G5P 0.504854 0.922078
59 APC G U 0.504425 0.909091
60 3AM 0.5 0.90411
61 JB2 0.5 0.910256
62 CG2 0.5 0.911392
63 GTG 0.5 0.8875
64 GDX 0.495238 0.922078
65 GPD 0.495238 0.876543
66 GPX 0.494845 0.92
67 GDP 7MG 0.490385 0.886076
68 DGI 0.48913 0.897436
69 JB3 0.486239 0.898734
70 G G G C 0.482759 0.8875
71 GGM 0.482143 0.876543
72 A G C C 0.478632 0.886076
73 C2E 0.478261 0.92
74 PCG 0.478261 0.932432
75 35G 0.478261 0.932432
76 A G U 0.47619 0.8875
77 5GP 5GP 0.473118 0.906667
78 2MD 0.469027 0.845238
79 DGT 0.46875 0.897436
80 FEG 0.468468 0.855422
81 NGD 0.468468 0.910256
82 DG DG 0.465347 0.8875
83 ZGP 0.464286 0.845238
84 G C C C 0.46281 0.898734
85 A G U U 0.458015 0.8875
86 MGD 0.456897 0.845238
87 GPC 0.456897 0.878049
88 AKW 0.455357 0.843373
89 CAG 0.444444 0.835294
90 PGD O 0.442623 0.806818
91 TPG 0.434426 0.797753
92 DBG 0.434426 0.898734
93 G1R G1R 0.434426 0.875
94 UCG 0.430894 0.910256
95 PGD 0.429752 0.876543
96 MD1 0.429752 0.845238
97 G1G 0.425 0.876543
98 FE9 0.421488 0.755319
99 4BW 0.416667 0.92
100 1YD 0.416667 0.92
101 3ZE 0.410526 0.858974
102 CGP 0.410256 0.888889
103 DC DG 0.40678 0.865854
104 A3P 0.402174 0.891892
105 G4M 0.401515 0.857143
Ligand no: 2; Ligand: SGP; Similar ligands found: 56
No: Ligand ECFP6 Tc MDL keys Tc
1 SGP 1 1
2 P2G 0.614458 0.907895
3 P1G 0.6 0.896104
4 GMP 0.576923 0.78481
5 GPX 0.56383 0.871795
6 3GP 0.517241 0.871795
7 2GP 0.517241 0.860759
8 5GP 0.488889 0.8375
9 G 0.488889 0.8375
10 QQX 0.488095 0.906667
11 PCG 0.483871 0.835443
12 35G 0.483871 0.835443
13 C2E 0.483871 0.825
14 5GP 5GP 0.463158 0.8125
15 GDP 0.463158 0.82716
16 1YC 0.457944 0.846154
17 GP3 0.452632 0.807229
18 GTP 0.44898 0.82716
19 GP2 0.447917 0.797619
20 GCP 0.444444 0.807229
21 GNH 0.443299 0.817073
22 KB7 0.443299 0.72093
23 GPG 0.442308 0.819277
24 GSP 0.44 0.876543
25 G2P 0.44 0.797619
26 G3D 0.44 0.8375
27 1YD 0.435185 0.825
28 4BW 0.435185 0.825
29 GMV 0.434343 0.807229
30 ALF 5GP 0.434343 0.758621
31 GAV 0.431373 0.864198
32 G4P 0.431373 0.8375
33 DGP 0.430108 0.817073
34 DG 0.430108 0.817073
35 G1R 0.43 0.817073
36 9GM 0.425743 0.807229
37 GNP 0.425743 0.807229
38 UCG 0.424 0.819277
39 GH3 0.421569 0.82716
40 DGI 0.418367 0.807229
41 0O2 0.415094 0.8375
42 DG DG 0.415094 0.77907
43 4UR 0.413793 0.825
44 GDC 0.412844 0.819277
45 GKE 0.412844 0.819277
46 Y9Z 0.412844 0.772727
47 GDD 0.412844 0.819277
48 KT2 0.411765 0.825
49 GDP ALF 0.409524 0.758621
50 GDP AF3 0.409524 0.758621
51 ALF GDP 0.409524 0.758621
52 G2R 0.40566 0.797619
53 G3A 0.405405 0.807229
54 DGT 0.401961 0.807229
55 KBD 0.401869 0.72093
56 G5P 0.401786 0.807229
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1RNT; Ligand: 2GP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 1rnt.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
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