Receptor
PDB id Resolution Class Description Source Keywords
5DUB 2 Å NON-ENZYME: OTHER CONTEXT-INDEPENDENT ANTI-HYPUSINE ANTIBODY FABHPU98 IN COMPL DEOXYHYPUSINE ORYCTOLAGUS CUNICULUS DEOXYHYPUSINE ANTIBODY FABHPU98 EIF5A IMMUNE SYSTEM
Ref.: STRUCTURAL ANALYSIS AND OPTIMIZATION OF CONTEXT-IND ANTI-HYPUSINE ANTIBODIES. J.MOL.BIOL. V. 428 603 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO B:302;
A:301;
B:306;
B:305;
H:302;
H:301;
A:304;
A:303;
A:302;
H:304;
B:301;
H:303;
B:303;
B:304;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
SO4 H:306;
A:308;
L:302;
H:307;
P:101;
B:308;
A:305;
A:309;
A:306;
H:305;
L:301;
A:307;
B:307;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
GLY 5GG GLY ALA P:3;
Valid;
Atoms found LESS than expected: % Diff = 0.036;
submit data
389.521 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5DUB 2 Å NON-ENZYME: OTHER CONTEXT-INDEPENDENT ANTI-HYPUSINE ANTIBODY FABHPU98 IN COMPL DEOXYHYPUSINE ORYCTOLAGUS CUNICULUS DEOXYHYPUSINE ANTIBODY FABHPU98 EIF5A IMMUNE SYSTEM
Ref.: STRUCTURAL ANALYSIS AND OPTIMIZATION OF CONTEXT-IND ANTI-HYPUSINE ANTIBODIES. J.MOL.BIOL. V. 428 603 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 5DUB - GLY 5GG GLY ALA n/a n/a
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 5DUB - GLY 5GG GLY ALA n/a n/a
50% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 3U7Y - FLC C6 H5 O7 C(C(=O)[O-....
2 1NC4 - DOF C23 H33 N5 O10 c1cc(ccc1C....
3 5DS8 - GLY 5CT GLY ALA n/a n/a
4 5DRN - 5CT C10 H23 N3 O3 C(CCNC[C@H....
5 3KDM Kd = 0.1 uM TES C19 H28 O2 C[C@]12CC[....
6 1QKZ - ALA ASN GLY GLY ALA SER GLY GLN VAL LYS n/a n/a
7 1NC2 - DOE C27 H41 N5 O10 S c1cc(ccc1C....
8 2HVK - TBA C16 H36 N CCCC[N+](C....
9 5DUB - GLY 5GG GLY ALA n/a n/a
10 5MES ic50 = 0.045 uM 7LT C44 H49 Cl2 N5 O4 CN1CCCN[C@....
11 1FE8 - NAG C8 H15 N O6 CC(=O)N[C@....
12 3LEV - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
13 5T85 - 44G C18 H35 O10 P CCCCCC(=O)....
14 1E4X Kd = 25 nM VAL VAL SER HIS PHE ASN ASP n/a n/a
15 4MA7 - P2Z C17 H20 N2 S CN(C)CCCN1....
16 4MA8 - Z80 C17 H19 Cl N2 S CN(C)CCCN1....
17 4DVR - 0LY C17 H24 Br N3 O2 CC1(CC(CC(....
18 4UUJ - XA7 C24 H52 N CCCCCC[N+]....
19 2DWE - TBA C16 H36 N CCCC[N+](C....
20 3PGF - GLC GLC n/a n/a
21 1MJJ Kd = 1.83 nM HAL C23 H29 N2 O7 P c1ccc(cc1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GLY 5GG GLY ALA; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 GLY 5GG GLY ALA 1 1
2 GLY 5CT GLY ALA 0.746479 0.880952
3 GLY 5CT GLY SER GLY 0.517647 0.777778
4 GLY GLY ALY ALA PRO ARG LYS GLN 0.425 0.9
5 GLY SER ILE THR THR LEU GLY LYS PHE GLY 0.421053 0.702128
6 ALA GLY ALA GLY ALA 0.408451 0.794872
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5DUB; Ligand: GLY 5GG GLY ALA; Similar sites found: 66
This union binding pocket(no: 1) in the query (biounit: 5dub.bio2) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1Z34 2FD 0.003505 0.48684 2.33645
2 1CR1 TTP 0.006556 0.48251 2.33645
3 3A8U PLP 0.0155 0.4262 2.33645
4 1WVC CTP 0.002542 0.51249 3.27103
5 4G1V FAD 0.004199 0.5047 3.27103
6 1F8F NAD 0.03082 0.43766 3.27103
7 4TMK T5A 0.0251 0.46493 3.28639
8 4NVP 7CH 0.02362 0.42901 3.34928
9 1UH4 GLC 0.01239 0.41324 3.6036
10 1JA9 PYQ 0.01183 0.43766 3.73832
11 1V1A KDG 0.009336 0.4316 3.73832
12 2XZ3 MAL 0.01732 0.42917 3.73832
13 2PAR TMP 0.03096 0.42969 3.9801
14 1OFH ADP 0.001861 0.50653 4.02299
15 3CXO 3LR 0.02695 0.4193 4.05405
16 3CXO 1N5 0.03626 0.41495 4.05405
17 2FWP ICR 0.03803 0.41809 4.37158
18 1JQ5 NAD 0.006485 0.50408 4.5045
19 1VQ2 DDN 0.007597 0.47515 4.66321
20 2IMP NAI 0.02861 0.45095 4.6729
21 1G7V PAI 0.01477 0.44371 4.6729
22 2IMP LAC 0.005411 0.44239 4.6729
23 3CL7 HYN 0.04536 0.40252 4.6729
24 1W55 GPP 0.001882 0.45625 4.95496
25 1W55 C 0.03151 0.43285 4.95496
26 1QCA FUA 0.01221 0.46568 5.16432
27 4TSK NDP 0.04133 0.43191 5.40541
28 2AEB ABH 0.04127 0.41469 5.40541
29 2W8Q SIN 0.02797 0.40711 5.54415
30 4I9A NCN 0.0384 0.41134 5.60748
31 2CCV A2G 0.0178 0.4246 5.94059
32 2YYJ 4HP 0.03849 0.44456 6.07477
33 2YYJ FAD 0.03849 0.44456 6.07477
34 3EM1 TYD 0.02858 0.41204 6.16438
35 1O6B ADP 0.0007448 0.51744 6.50888
36 1XMV ADP 0.0003761 0.53917 6.54206
37 3RO7 TDR 0.01307 0.47646 6.54206
38 3D3W NAP 0.03493 0.4158 6.54206
39 3LIH RAF 0.03252 0.40216 6.54206
40 2GJ3 FAD 0.004321 0.49617 6.66667
41 4HGP KDO 0.04363 0.41493 6.66667
42 2P8B NSK 0.009126 0.48929 6.75676
43 4LBP 1WG 0.04145 0.40962 7
44 4KCF AKM 0.01416 0.45324 7.20721
45 1C4U IH1 0.003923 0.44831 7.20721
46 4KCF FMN 0.01791 0.43735 7.20721
47 2X61 CH 0.02656 0.42422 7.20721
48 1A78 TDG 0.001778 0.45072 7.46269
49 1SAZ ACP 0.01975 0.45906 7.47664
50 2QS8 MET 0.02306 0.42022 7.47664
51 1NVU GTP 0.02494 0.44272 7.65766
52 2YMZ LAT 0.001244 0.41251 7.69231
53 3CKZ ZMR 0.03336 0.42668 7.94393
54 2V9M CIT 0.01651 0.4064 7.94393
55 1GSA ADP 0.0458 0.42398 8.10811
56 4Q3R XA2 0.04521 0.40393 8.8785
57 3K9W 4PS 0.003491 0.50928 9.09091
58 3K9W ADE 0.003491 0.50928 9.09091
59 1BDB NAD 0.04975 0.43424 9.90991
60 1NPL MAN 0.007853 0.43788 10.0917
61 1ZFJ IMP 0.003393 0.51047 10.7477
62 2BGM NAJ 0.03642 0.43496 11.6822
63 2BLE 5GP 0.04532 0.43092 11.7117
64 1G6O ADP 0.002139 0.50089 16.2162
65 1Q3Q ANP 0.04388 0.42917 16.8224
66 4EKV BTN 0.04942 0.41004 17.6101
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