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 HOMOLOGUE) COMPLEXED WITH A GUANYLYL-3',5'-CYTIDINE A NALOGUE ASPERGILLUS PHOENICIS HYDROLASE(ENDORIBONUCLEASE)
Ref.: CRYSTAL STRUCTURE OF RIBONUCLEASE MS (AS A RIBONUCLEASE T1 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 HOMOLOGUE) COMPLEXED WITH A GUANYLYL-3',5'-CYTIDINE A NALOGUE ASPERGILLUS PHOENICIS HYDROLASE(ENDORIBONUCLEASE)
Ref.: CRYSTAL STRUCTURE OF RIBONUCLEASE MS (AS A RIBONUCLEASE T1 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: 108
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 OMC OMU OMG OMG U 0.544218 0.873563
11 CDP 0.509091 0.819277
12 GNH 0.5 0.869048
13 CGP 0.5 0.895349
14 G3D 0.495868 0.86747
15 CDM 0.495868 0.764045
16 CTP 0.495575 0.819277
17 UCG 0.493056 0.915663
18 C5G 0.491803 0.821429
19 GDP 0.491525 0.879518
20 7XL 0.491379 0.8
21 G4P 0.487805 0.86747
22 0O2 0.484127 0.86747
23 GSP 0.483607 0.83908
24 GP3 0.483051 0.880952
25 2GP 0.482456 0.86747
26 CAR 0.481481 0.829268
27 C 0.481481 0.829268
28 C5P 0.481481 0.829268
29 A G U 0.480263 0.916667
30 GTP 0.479339 0.879518
31 C2G 0.478992 0.809524
32 GCP 0.47541 0.858824
33 91P 0.474453 0.895349
34 G 0.474138 0.890244
35 5GP 0.474138 0.890244
36 GKE 0.469231 0.892857
37 GDC 0.469231 0.892857
38 GDD 0.469231 0.892857
39 CSQ 0.46875 0.811765
40 CSV 0.46875 0.811765
41 GMV 0.467213 0.858824
42 JB2 0.466165 0.870588
43 G1R 0.463415 0.869048
44 G U34 0.460432 0.916667
45 GNP 0.459677 0.858824
46 3GP 0.456897 0.878049
47 GP2 0.454545 0.848837
48 FN5 0.453237 0.848837
49 G2R 0.453125 0.848837
50 GAV 0.452381 0.848837
51 CXY 0.452381 0.8
52 CDC 0.451613 0.712766
53 YGP 0.450382 0.883721
54 TPG 0.445946 0.808511
55 DC DG 0.443662 0.873563
56 GFB 0.443609 0.870588
57 GDR 0.443609 0.870588
58 GMP 0.441441 0.795181
59 6CK 0.440298 0.916667
60 G2P 0.436508 0.848837
61 Y9Z 0.43609 0.822222
62 G G 0.435115 0.869048
63 A U C C 0.435065 0.880952
64 GKD 0.433824 0.892857
65 UPU 0.433333 0.792683
66 GTG 0.432836 0.850575
67 FEG 0.432624 0.822222
68 ALF 5GP 0.432 0.872093
69 GPD 0.430657 0.840909
70 GDX 0.430657 0.880952
71 U G A 0.43038 0.916667
72 G3A 0.42963 0.880952
73 ZGP 0.429577 0.813187
74 C C 0.427419 0.807229
75 CDP MG 0.42735 0.767442
76 DG DC 0.426667 0.862069
77 G5P 0.426471 0.880952
78 JB3 0.425532 0.860465
79 1AA 0.425373 0.835294
80 GDP MG 0.424 0.837209
81 BEF GDP 0.421875 0.850575
82 U A C C 0.421769 0.869048
83 GDP BEF 0.420635 0.860465
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 CTN 0.415094 0.722892
89 AR3 0.415094 0.722892
90 PGD 0.413333 0.862069
91 P2G 0.413223 0.821429
92 G G U 0.413043 0.869048
93 NGD 0.412587 0.870588
94 GDP AF3 0.412214 0.872093
95 GDP ALF 0.412214 0.872093
96 CSF 0.410959 0.848837
97 GH3 0.410853 0.857143
98 GTP MG 0.410853 0.837209
99 DGI 0.408 0.816092
100 GCP G 0.407692 0.847059
101 C3P 0.40708 0.817073
102 2AA 0.406897 0.672897
103 DGT 0.40625 0.816092
104 CAG 0.405405 0.804348
105 BGO 0.402778 0.83908
106 I2C FE2 CMO CMO 0.402685 0.797872
107 PMT 0.401408 0.75
108 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: 35
This union binding pocket(no: 1) in the query (biounit: 1rds.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2XK9 XK9 0.00737 0.43043 None
2 3RI1 3RH 0.01516 0.40788 None
3 4BUZ OAD 0.01901 0.40684 None
4 2XVD AS6 0.01732 0.40508 None
5 4BUZ OCZ 0.02429 0.40164 None
6 4BUZ NAD 0.02076 0.4013 None
7 4MPO AMP 0.009269 0.4017 1.90476
8 3DGY 2GP 0.000008975 0.57209 2.06186
9 1MO9 KPC 0.02431 0.43359 4.7619
10 4V03 ADP 0.004495 0.41355 4.7619
11 4GYI ADP 0.01034 0.40105 4.7619
12 3BFV ADP 0.01234 0.40149 5.71429
13 3AKK ADP 0.005879 0.41453 6.66667
14 5EOB 5QQ 0.03286 0.41208 6.66667
15 5IXJ THR 0.02481 0.40849 6.66667
16 4DXJ 0M9 0.002861 0.44402 7.61905
17 4DXJ IPE 0.003265 0.44397 7.61905
18 4EUU BX7 0.009473 0.41487 7.61905
19 1XFF GLU 0.006536 0.41028 7.61905
20 4C2V YJA 0.01886 0.40458 7.61905
21 4NST ADP 0.009547 0.40291 7.61905
22 2X4Z X4Z 0.006635 0.4315 8.57143
23 1N0U SO1 0.004797 0.4186 8.57143
24 3G5D 1N1 0.02928 0.41538 8.57143
25 2OFV 242 0.02098 0.4081 8.57143
26 5K2M ADP 0.01601 0.40109 8.57143
27 5UIU 8CG 0.01694 0.40683 9.52381
28 4CZG ADP 0.01973 0.40942 11.4286
29 5GQX GLC GLC GLC GLC 0.03895 0.4013 11.4286
30 3W5J GDP 0.01374 0.41307 12.381
31 2XMY CDK 0.0146 0.43648 13.3333
32 4GJ3 0XP 0.01564 0.40976 15.2381
33 3PE2 E1B 0.03853 0.4032 16.1905
34 3DNT ATP 0.007046 0.4179 20
35 1ION ADP 0.004576 0.4132 28.5714
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