Receptor
PDB id Resolution Class Description Source Keywords
1HZ1 1.8 Å EC: 3.1.27.3 RIBONUCLEASE T1 V16A MUTANT IN COMPLEX WITH MG2+ ASPERGILLUS NIGER RIBONUCLEASE METAL BINDING STABILITY HYDROLASE
Ref.: THE CONTRIBUTION OF METAL IONS TO THE CONFORMATIONAL STABILITY OF RIBONUCLEASE T1: CRYSTAL VERSUS SOLUTION. EUR.J.BIOCHEM. V. 268 3993 2001
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
2GP A:106;
 Valid;
 none;
 submit data
363.221 C10 H14 N5 O8 P c1nc2...
MG A:105;
 Part of Protein;
 none;
 submit data
24.305 Mg [Mg+2...
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 OF THE RIBONUCLEASE T1(ASTERISK)2(PRIME)- G UANYLIC ACID COMPLEX AT 1.9 ANGSTROMS RESOLUTION ASPERGILLUS ORYZAE HYDROLASE(ENDORIBONUCLEASE)
Ref.: RESTRAINED LEAST-SQUARES REFINEMENT OF THE CRYSTAL STRUCTURE OF THE RIBONUCLEASE T1(ASTERISK)2(PRIME)-GUANYLIC ACID 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: 2GP; Similar ligands found: 95
No: Ligand ECFP6 Tc MDL keys Tc
1 2GP 1 1
2 3GP 0.733333 0.959459
3 GPG 0.701149 0.948052
4 GMP 0.657534 0.866667
5 G3D 0.613636 0.972973
6 G 0.609756 0.946667
7 5GP 0.609756 0.946667
8 P2G 0.590361 0.92
9 GSP 0.577778 0.911392
10 GDP 0.574713 0.96
11 GNH 0.568182 0.947368
12 G4P 0.565217 0.972973
13 GP3 0.563218 0.935065
14 P1G 0.55814 0.907895
15 GP2 0.556818 0.923077
16 GTP 0.555556 0.96
17 G2P 0.543478 0.923077
18 0O2 0.541667 0.972973
19 GMV 0.538462 0.935065
20 GDC 0.535354 0.948052
21 GKE 0.535354 0.948052
22 GDD 0.535354 0.948052
23 G1R 0.532609 0.947368
24 GCP 0.532609 0.935065
25 GAV 0.531915 0.923077
26 GDP MG 0.527473 0.886076
27 GNP 0.526882 0.935065
28 ALF 5GP 0.521739 0.853659
29 GDP BEF 0.521739 0.864198
30 SGP 0.517241 0.860759
31 CG2 0.513761 0.924051
32 U2G 0.509259 0.924051
33 DGP 0.505747 0.922078
34 DG 0.505747 0.922078
35 GTP MG 0.505263 0.886076
36 GH3 0.505263 0.96
37 BEF GDP 0.505263 0.853659
38 G G 0.50505 0.897436
39 G2R 0.5 0.923077
40 GCP G 0.5 0.897436
41 GKD 0.5 0.948052
42 GPX 0.494845 0.959459
43 GDP ALF 0.489796 0.853659
44 GDP AF3 0.489796 0.853659
45 DGI 0.48913 0.935065
46 2AM 0.487805 0.905405
47 GFB 0.485437 0.923077
48 GDR 0.485437 0.923077
49 GPC 0.482456 0.86747
50 G C 0.482143 0.8875
51 6CK 0.480769 0.9
52 G3A 0.480769 0.935065
53 YGP 0.480392 0.865854
54 G U34 0.477477 0.876543
55 G5P 0.47619 0.935065
56 Y9Z 0.475728 0.890244
57 G G U 0.471698 0.922078
58 JB2 0.471698 0.923077
59 GTG 0.471154 0.9
60 DGT 0.46875 0.935065
61 GDX 0.46729 0.935065
62 GPD 0.46729 0.888889
63 JB3 0.459459 0.911392
64 G G G RPC 0.45614 0.8625
65 BGO 0.455357 0.911392
66 G A A A 0.452174 0.910256
67 DG DG 0.45098 0.876543
68 G1G 0.449153 0.888889
69 GDP 7MG 0.448598 0.875
70 35G 0.446809 0.92
71 C2E 0.446809 0.907895
72 PCG 0.446809 0.92
73 FEG 0.442478 0.845238
74 5GP 5GP 0.442105 0.87013
75 ZGP 0.438596 0.835294
76 U A G G 0.435897 0.897436
77 G G G C 0.433333 0.876543
78 2MD 0.431034 0.857143
79 GGM 0.431034 0.888889
80 UCG 0.430894 0.898734
81 NGD 0.429825 0.923077
82 A G C C 0.429752 0.875
83 APC G U 0.428571 0.873418
84 TPG 0.422764 0.808989
85 OVE 0.420455 0.87013
86 CAG 0.420168 0.847059
87 G C C C 0.416 0.8875
88 3ZE 0.410526 0.848101
89 MGD 0.408333 0.857143
90 PGD 0.406504 0.888889
91 4BW 0.40367 0.907895
92 1YD 0.40367 0.907895
93 OMC OMU OMG OMG U 0.402985 0.833333
94 A2P 0.402174 0.891892
95 DBG 0.4 0.911392
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1RNT; Ligand: 2GP; Similar sites found: 13
This union binding pocket(no: 1) in the query (biounit: 1rnt.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4V03 ADP 0.006933 0.41123 None
2 4DXJ 0M9 0.01321 0.40199 None
3 4DXJ IPE 0.01603 0.40064 None
4 3LQV ADE 0.005034 0.44133 3.84615
5 2XK9 XK9 0.0158 0.40434 4.80769
6 2X4Z X4Z 0.01621 0.40271 7.69231
7 3ZS9 ADP ALF 0.00919 0.40193 7.69231
8 4GYI ADP 0.008829 0.41032 8.65385
9 5LNE A2G GAL 0.01464 0.40928 9.61539
10 3DGY 2GP 0.000001197 0.62686 10.3093
11 4AXD ANP 0.01309 0.41024 10.5769
12 4N70 2HX 0.01939 0.41048 11.5385
13 3BFV ADP 0.01469 0.40377 26.9231
Feedback