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Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GPC A:106;
Valid;
none;
submit data
590.413 C19 H24 F N8 O11 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: GPC; Similar ligands found: 106
No: Ligand ECFP6 Tc MDL keys Tc
1 GPC 1 1
2 CG2 0.68595 0.939759
3 G C 0.680328 0.927711
4 G G G C 0.635659 0.916667
5 A G C C 0.618321 0.915663
6 G C C C 0.61194 0.927711
7 U2G 0.565891 0.939759
8 GPG 0.558333 0.892857
9 G G G RPC 0.55303 0.880952
10 G U 0.537879 0.927711
11 CDP 0.509091 0.819277
12 GNH 0.5 0.869048
13 CGP 0.5 0.895349
14 CDM 0.495868 0.764045
15 G3D 0.495868 0.86747
16 HF4 0.495575 0.819277
17 CTP 0.495575 0.819277
18 UCG 0.493056 0.915663
19 C5G 0.491803 0.821429
20 GDP 0.491525 0.879518
21 7XL 0.491379 0.8
22 G4P 0.487805 0.86747
23 0O2 0.484127 0.86747
24 GSP 0.483607 0.83908
25 GP3 0.483051 0.880952
26 2GP 0.482456 0.86747
27 C5P 0.481481 0.829268
28 C 0.481481 0.829268
29 CAR 0.481481 0.829268
30 A G U 0.480263 0.916667
31 GTP 0.479339 0.879518
32 C2G 0.478992 0.809524
33 GCP 0.47541 0.858824
34 91P 0.474453 0.895349
35 G 0.474138 0.890244
36 5GP 0.474138 0.890244
37 GDD 0.469231 0.892857
38 GKE 0.469231 0.892857
39 GDC 0.469231 0.892857
40 CSV 0.46875 0.811765
41 CSQ 0.46875 0.811765
42 GMV 0.467213 0.858824
43 JB2 0.466165 0.870588
44 A G U U 0.464968 0.916667
45 G1R 0.463415 0.869048
46 G U34 0.460432 0.916667
47 GNP 0.459677 0.858824
48 9GM 0.459677 0.858824
49 3GP 0.456897 0.878049
50 GP2 0.454545 0.848837
51 FN5 0.453237 0.848837
52 G2R 0.453125 0.848837
53 CXY 0.452381 0.8
54 GAV 0.452381 0.848837
55 C C C C 0.451613 0.819277
56 CDC 0.451613 0.712766
57 YGP 0.450382 0.883721
58 TPG 0.445946 0.808511
59 DC DG 0.443662 0.873563
60 GFB 0.443609 0.870588
61 GDR 0.443609 0.870588
62 GMP 0.441441 0.795181
63 6CK 0.440298 0.916667
64 G2P 0.436508 0.848837
65 Y9Z 0.43609 0.822222
66 A U C C 0.435065 0.880952
67 GKD 0.433824 0.892857
68 UPU 0.433333 0.792683
69 G G 0.432836 0.880952
70 GTG 0.432836 0.850575
71 FEG 0.432624 0.822222
72 ALF 5GP 0.432 0.872093
73 A C A C 0.431507 0.880952
74 GDX 0.430657 0.880952
75 GPD 0.430657 0.840909
76 G3A 0.42963 0.880952
77 ZGP 0.429577 0.813187
78 C C 0.427419 0.807229
79 DG DC 0.426667 0.862069
80 G5P 0.426471 0.880952
81 JB3 0.425532 0.860465
82 1AA 0.425373 0.835294
83 U A C C 0.421769 0.869048
84 G1G 0.418919 0.840909
85 P1G 0.418033 0.811765
86 FE9 0.416107 0.767677
87 GPX 0.415385 0.833333
88 AR3 0.415094 0.722892
89 CTN 0.415094 0.722892
90 GCP G 0.413534 0.833333
91 PGD 0.413333 0.862069
92 P2G 0.413223 0.821429
93 NGD 0.412587 0.870588
94 ALF GDP 0.412214 0.872093
95 GDP AF3 0.412214 0.872093
96 GDP ALF 0.412214 0.872093
97 CSF 0.410959 0.848837
98 GH3 0.410853 0.857143
99 DGI 0.408 0.816092
100 C3P 0.40708 0.817073
101 2AA 0.406897 0.672897
102 DGT 0.40625 0.816092
103 CAG 0.405405 0.804348
104 BGO 0.402778 0.83908
105 PMT 0.401408 0.75
106 G A A A 0.401361 0.880952
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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