Receptor
PDB id Resolution Class Description Source Keywords
1RMS 1.9 Å EC: 3.1.4.23 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: 3.1.4.23 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 1 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 = 49.1 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 = 49.1 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 (2D)
Ligand no: 1; Ligand: 3GP; Similar ligands found: 92
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 5GP 0.65 0.959459
7 G 0.65 0.959459
8 0O2 0.644444 0.959459
9 GDP 0.611765 0.946667
10 GNH 0.604651 0.934211
11 GP3 0.6 0.922078
12 GSP 0.595506 0.898734
13 GP2 0.593023 0.910256
14 GPG 0.591398 0.935065
15 GTP 0.590909 0.946667
16 G2P 0.577778 0.910256
17 GMV 0.573034 0.922078
18 ALF 5GP 0.573034 0.864198
19 P2G 0.571429 0.932432
20 GKE 0.56701 0.935065
21 GDD 0.56701 0.935065
22 GDC 0.56701 0.935065
23 GCP 0.566667 0.922078
24 GDP BEF 0.566667 0.909091
25 G1R 0.566667 0.934211
26 G C 0.566038 0.898734
27 GAV 0.565217 0.910256
28 GNP 0.56044 0.922078
29 GTP MG 0.56044 0.933333
30 9GM 0.56044 0.922078
31 P1G 0.55814 0.92
32 GDP ALF 0.536842 0.864198
33 GDP AF3 0.536842 0.864198
34 KB7 0.533333 0.825
35 G2R 0.53125 0.910256
36 KBD 0.525773 0.825
37 SGP 0.517241 0.871795
38 GDR 0.514852 0.910256
39 GFB 0.514852 0.910256
40 GKD 0.514563 0.935065
41 YGP 0.51 0.876543
42 G3A 0.509804 0.922078
43 6CK 0.509804 0.8875
44 BGO 0.509259 0.898734
45 U2G 0.509259 0.911392
46 DG 0.505747 0.909091
47 DGP 0.505747 0.909091
48 GH3 0.505263 0.946667
49 KBJ 0.504951 0.795181
50 Y9Z 0.504951 0.878049
51 G5P 0.504854 0.922078
52 JB2 0.5 0.910256
53 CG2 0.5 0.911392
54 3AM 0.5 0.90411
55 GTG 0.5 0.8875
56 GDX 0.495238 0.922078
57 GPD 0.495238 0.876543
58 GPX 0.494845 0.92
59 APC G U 0.491379 0.909091
60 GDP 7MG 0.490385 0.886076
61 DGI 0.48913 0.897436
62 JB3 0.486239 0.898734
63 GGM 0.482143 0.876543
64 35G 0.478261 0.932432
65 C2E 0.478261 0.92
66 PCG 0.478261 0.932432
67 5GP 5GP 0.473118 0.906667
68 2MD 0.469027 0.845238
69 DGT 0.46875 0.897436
70 NGD 0.468468 0.910256
71 FEG 0.468468 0.855422
72 ZGP 0.464286 0.845238
73 GPC 0.456897 0.878049
74 MGD 0.456897 0.845238
75 AKW 0.455357 0.843373
76 CAG 0.444444 0.835294
77 PGD O 0.442623 0.806818
78 TPG 0.434426 0.797753
79 DBG 0.434426 0.898734
80 G1R G1R 0.434426 0.875
81 I2C FE2 CMO CMO 0.433333 0.786517
82 UCG 0.430894 0.910256
83 MD1 0.429752 0.845238
84 PGD 0.429752 0.876543
85 G1G 0.425 0.876543
86 FE9 0.421488 0.755319
87 4BW 0.416667 0.92
88 1YD 0.416667 0.92
89 3ZE 0.410526 0.858974
90 CGP 0.410256 0.888889
91 A3P 0.402174 0.891892
92 G4M 0.401515 0.857143
Similar Ligands (3D)
Ligand no: 1; Ligand: 3GP; Similar ligands found: 32
No: Ligand Similarity coefficient
1 101 0.9386
2 A3G 0.9375
3 103 0.9276
4 CMP 0.9217
5 75G 0.9176
6 T3P 0.9095
7 A3S 0.9055
8 SP1 0.9044
9 7CH 0.9028
10 RP1 0.9016
11 UA3 0.9000
12 6J7 0.8997
13 6SW 0.8990
14 U3P 0.8988
15 UMF 0.8935
16 6SZ 0.8900
17 ACK 0.8900
18 C3P 0.8870
19 8MF 0.8855
20 6SX 0.8805
21 TMP 0.8801
22 2AM 0.8781
23 4UO 0.8764
24 2FA 0.8762
25 CD9 0.8724
26 IMV 0.8699
27 GNG 0.8654
28 CL9 0.8637
29 ADN 0.8614
30 KUP 0.8567
31 BGC BGC 0.8546
32 QRP 0.8518
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: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 1rds.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
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