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Receptor
PDB id Resolution Class Description Source Keywords
1RMS 1.9 Å EC: 3.1.27.3 CRYSTAL STRUCTURES OF RIBONUCLEASE MS COMPLEXED WITH 3'-GUAN A GP*C ANALOGUE, 2'-DEOXY-2'-FLUOROGUANYLYL-3',5'-CYTIDINE ASPERGILLUS PHOENICIS HYDROLASE(ENDORIBONUCLEASE)
Ref.: CRYSTAL STRUCTURE OF RIBONUCLEASE MS (AS A RIBONUCL HOMOLOGUE) COMPLEXED WITH A GUANYLYL-3',5'-CYTIDINE ANALOGUE. BIOCHEMISTRY V. 32 11825 1993
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...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1RDS 1.8 Å EC: 3.1.27.3 CRYSTAL STRUCTURE OF RIBONUCLEASE MS (AS RIBONUCLEASE T1 HOM COMPLEXED WITH A GUANYLYL-3',5'-CYTIDINE ANALOGUE ASPERGILLUS PHOENICIS HYDROLASE(ENDORIBONUCLEASE)
Ref.: CRYSTAL STRUCTURE OF RIBONUCLEASE MS (AS A RIBONUCL HOMOLOGUE) COMPLEXED WITH A GUANYLYL-3',5'-CYTIDINE ANALOGUE. BIOCHEMISTRY V. 32 11825 1993
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1RMS - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
2 1RDS - GPC C19 H24 F N8 O11 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: 102
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 GDD 0.56701 0.935065
26 GKE 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 ALF GDP 0.536842 0.864198
36 GDP AF3 0.536842 0.864198
37 GDP ALF 0.536842 0.864198
38 G2R 0.53125 0.910256
39 A G 0.518182 0.909091
40 SGP 0.517241 0.871795
41 GDR 0.514852 0.910256
42 GFB 0.514852 0.910256
43 GKD 0.514563 0.935065
44 U A G G 0.513514 0.909091
45 YGP 0.51 0.876543
46 6CK 0.509804 0.8875
47 G3A 0.509804 0.922078
48 U2G 0.509259 0.911392
49 BGO 0.509259 0.898734
50 G G G RPC 0.509091 0.897436
51 DG 0.505747 0.909091
52 DGP 0.505747 0.909091
53 GH3 0.505263 0.946667
54 Y9Z 0.504951 0.878049
55 G5P 0.504854 0.922078
56 APC G U 0.504425 0.909091
57 GTG 0.5 0.8875
58 CG2 0.5 0.911392
59 3AM 0.5 0.90411
60 JB2 0.5 0.910256
61 GDX 0.495238 0.922078
62 GPD 0.495238 0.876543
63 GPX 0.494845 0.92
64 GDP 7MG 0.490385 0.886076
65 DGI 0.48913 0.897436
66 JB3 0.486239 0.898734
67 G G G C 0.482759 0.8875
68 GGM 0.482143 0.876543
69 A G C C 0.478632 0.886076
70 35G 0.478261 0.932432
71 C2E 0.478261 0.92
72 PCG 0.478261 0.932432
73 A G U 0.47619 0.8875
74 5GP 5GP 0.473118 0.906667
75 2MD 0.469027 0.845238
76 DGT 0.46875 0.897436
77 NGD 0.468468 0.910256
78 FEG 0.468468 0.855422
79 DG DG 0.465347 0.8875
80 ZGP 0.464286 0.845238
81 G C C C 0.46281 0.898734
82 A G U U 0.458015 0.8875
83 MGD 0.456897 0.845238
84 GPC 0.456897 0.878049
85 AKW 0.455357 0.843373
86 CAG 0.444444 0.835294
87 PGD O 0.442623 0.806818
88 DBG 0.434426 0.898734
89 G1R G1R 0.434426 0.875
90 TPG 0.434426 0.797753
91 UCG 0.430894 0.910256
92 MD1 0.429752 0.845238
93 PGD 0.429752 0.876543
94 G1G 0.425 0.876543
95 FE9 0.421488 0.755319
96 4BW 0.416667 0.92
97 1YD 0.416667 0.92
98 3ZE 0.410526 0.858974
99 CGP 0.410256 0.888889
100 DC DG 0.40678 0.865854
101 A3P 0.402174 0.891892
102 G4M 0.401515 0.857143
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1RDS; Ligand: GPC; Similar sites found with APoc: 82
This union binding pocket(no: 1) in the query (biounit: 1rds.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 2XK9 XK9 None
2 2XVD AS6 None
3 4BUZ OAD None
4 4BUZ OCZ None
5 4BUZ NAD None
6 5WO4 B7V 1.90476
7 5HCY 60D 1.90476
8 3FC2 IBI 1.90476
9 4MPO AMP 1.90476
10 3DGY 2GP 2.06186
11 5NKB 8ZT 2.85714
12 4AP9 1PS 2.85714
13 4EWH T77 2.85714
14 3KP6 SAL 3.80952
15 5TO8 7FM 3.80952
16 1MO9 KPC 4.7619
17 1MO9 FAD 4.7619
18 5DY5 5GR 4.7619
19 4V03 ADP 4.7619
20 4PU5 ANP 4.7619
21 4Z4P SAH 4.7619
22 1JG9 GLC 4.7619
23 4GYI ADP 4.7619
24 3ZS9 ADP ALF 5.71429
25 4NFE BEN 5.71429
26 2JLD AG1 5.71429
27 5DEY 59T 5.71429
28 1ZX5 LFR 5.71429
29 3BFV ADP 5.71429
30 4KS7 X4Z 6.66667
31 3AKK ADP 6.66667
32 5VC5 96M 6.66667
33 5EOB 5QQ 6.66667
34 4CRL C1I 6.66667
35 3QFA FAD 6.66667
36 4DXJ 0M9 7.61905
37 4DXJ IPE 7.61905
38 4WHZ 3NL 7.61905
39 4EUU BX7 7.61905
40 5EYK 5U5 7.61905
41 4C2V YJA 7.61905
42 5EFQ ADP 7.61905
43 4QMN DB8 7.61905
44 2PVN P63 7.61905
45 4NST ADP 7.61905
46 1XFF GLU 7.61905
47 3H9R TAK 7.61905
48 5XVG 8FX 8.57143
49 5EW9 5VC 8.57143
50 1N0U SO1 8.57143
51 3G5D 1N1 8.57143
52 5YW5 ADE 8.57143
53 2OFV 242 8.57143
54 5K2M ADP 8.57143
55 3LXK MI1 9.52381
56 1VJY 460 9.52381
57 4A4X JUP 9.52381
58 5UIU 8CG 9.52381
59 5NC1 NAG 9.52381
60 6E8I PTR 10.4762
61 3E5A VX6 11.3636
62 4CZG ADP 11.4286
63 5GQX GLC GLC GLC GLC 11.4286
64 3W5J GDP 12.381
65 5C9P FUC 12.381
66 6GIN IR2 12.381
67 2XMY CDK 13.3333
68 3FHR P4O 13.3333
69 4E1Z 0MX 13.3333
70 1Y57 MPZ 13.3333
71 2BEK ATP 14.2857
72 4GJ3 0XP 15.2381
73 5K0A FAD 15.2381
74 4N70 2HX 17.1429
75 3EKK GS2 17.1429
76 4UUW AMP 17.1429
77 5WHU SIA GAL GLC 20
78 3DNT ATP 20
79 1GPE FAD 25.7143
80 5HQ0 LZ9 25.7143
81 1ION ADP 28.5714
82 4XZ3 ACP 28.5714
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