Receptor
PDB id Resolution Class Description Source Keywords
5YD3 1.35 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE SCFV ANTIBODY 4B08 WITH EPITOPE PEP MUS MUSCULUS ANTIBODY BIOMOLECULAR RECOGNITION MD SIMULATIONS THERMODYIMMUNE SYSTEM
Ref.: INTRAMOLECULAR H-BONDS GOVERN THE RECOGNITION OF A PEPTIDE BY AN ANTIBODY J. BIOCHEM. V. 164 65 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:302;
E:303;
G:301;
A:301;
A:304;
E:301;
A:303;
E:304;
E:302;
C:301;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
ASP ILE ASN TYR TYR THR SER GLU PRO H:3;
D:2;
B:2;
F:1;
Valid;
Valid;
Valid;
Valid;
Atoms found MORE than expected: % Diff = 1.333;
Atoms found LESS than expected: % Diff = 0.103;
Atoms found LESS than expected: % Diff = 0.103;
none;
Kd = 480 nM
1099.12 n/a O=C(N...
GOL A:305;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5YY4 1.59 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE SCFV ANTIBODY 4B08 WITH SULFATED EP PEPTIDE MUS MUSCULUS ANTIBODY BIOMOLECULAR RECOGNITION MD SIMULATIONS THERMODYIMMUNE SYSTEM
Ref.: TYROSINE SULFATION RESTRICTS THE CONFORMATIONAL ENS A FLEXIBLE PEPTIDE, STRENGTHENING THE BINDING AFFIN AN ANTIBODY BIOCHEMISTRY V. 57 4177 2018
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 5YD4 Kd = 13 uM ASP ILE ASN TYR TYR ALA SER GLU PRO n/a n/a
2 5YY4 Kd = 140 nM ASP ILE ASN TYS TYS THR SER GLU PRO n/a n/a
3 5YD3 Kd = 480 nM ASP ILE ASN TYR TYR THR SER GLU PRO n/a n/a
4 5YD5 Kd = 1.3 uM ASP ILE ALA TYR TYR THR SER GLU PRO n/a n/a
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 5YD4 Kd = 13 uM ASP ILE ASN TYR TYR ALA SER GLU PRO n/a n/a
2 5YY4 Kd = 140 nM ASP ILE ASN TYS TYS THR SER GLU PRO n/a n/a
3 5YD3 Kd = 480 nM ASP ILE ASN TYR TYR THR SER GLU PRO n/a n/a
4 5YD5 Kd = 1.3 uM ASP ILE ALA TYR TYR THR SER GLU PRO n/a n/a
5 4H0I - MMA C7 H14 O6 CO[C@@H]1[....
6 5VF2 - GLC GLC n/a n/a
50% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 4GQP Kd = 0.79 nM B40 C10 H15 N C[C@@H](Cc....
2 3GKZ Kd = 10 nM B40 C10 H15 N C[C@@H](Cc....
3 3GM0 Kd = 17 nM B41 C11 H15 N O2 C[C@@H](Cc....
4 5YD4 Kd = 13 uM ASP ILE ASN TYR TYR ALA SER GLU PRO n/a n/a
5 5YY4 Kd = 140 nM ASP ILE ASN TYS TYS THR SER GLU PRO n/a n/a
6 5YD3 Kd = 480 nM ASP ILE ASN TYR TYR THR SER GLU PRO n/a n/a
7 5YD5 Kd = 1.3 uM ASP ILE ALA TYR TYR THR SER GLU PRO n/a n/a
8 6QB9 - TLA C4 H6 O6 [C@@H]([C@....
9 4H0I - MMA C7 H14 O6 CO[C@@H]1[....
10 5VF2 - GLC GLC n/a n/a
11 5J75 Ki = 0.63 nM 6GQ C19 H24 N4 O3 S Cc1ccc(cc1....
12 5A2K - ALA PRO ASP THR ARG PRO A2G n/a n/a
13 6FRJ Kd = 141 uM ALA PRO ASP T9E ARG PRO NH2 A2G n/a n/a
14 5A2L - ALA PRO ASP CYS ARG PRO A2G n/a n/a
15 5A2I - ALA PRO ASP SER ARG PRO A2G n/a n/a
16 6FZR - ALA PRO ASP THR ARG PRO EEQ n/a n/a
17 6FZQ - ALA PRO ASP THR ARG PRO EEN n/a n/a
18 5A2J - ALA PRO ASP THR ARG PRO n/a n/a
19 5FXC - ALA PRO ASP THR ARG PRO n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: ASP ILE ASN TYR TYR THR SER GLU PRO; Similar ligands found: 116
No: Ligand ECFP6 Tc MDL keys Tc
1 ASP ILE ASN TYR TYR THR SER GLU PRO 1 1
2 ASP ILE ASN TYR TYR ALA SER GLU PRO 0.860656 1
3 ASP ILE ALA TYR TYR THR SER GLU PRO 0.716535 0.985075
4 ASP TYR ILE ASN THR ASN VAL LEU PRO 0.707692 0.926471
5 ASP ILE ASN TYS TYS THR SER GLU PRO 0.69697 0.817073
6 PHE TYR ALA PRO GLU PRO ILE THR SER LEU 0.562092 0.942857
7 THR PRO TYR ASP ILE ASN GLN MET LEU 0.529032 0.875
8 ASP PHE ALA ASN THR PHE LEU PRO 0.524476 0.911765
9 ILE SER TYR GLY ASN ASP ALA LEU MET PRO 0.522013 0.902778
10 GLN ILE MET TYR ASN TYR PRO ALA MET 0.516129 0.875
11 GLU GLU PRO THR VAL ILE LYS LYS TYR 0.496815 0.898551
12 HIS SER ILE THR TYR LEU LEU PRO VAL 0.49375 0.915493
13 ASP TYR GLU PRO ILE PRO GLU GLU ALA PHE 0.493671 0.911765
14 GLN ASN TYR PRO ILE VAL GLN 0.493151 0.897059
15 LEU ASN PHE PRO ILE SER PRO 0.489362 0.898551
16 GLU PRO VAL GLU THR THR ASP TYR 0.486301 0.882353
17 SER ASP PTR MET ASN MET THR PRO 0.48366 0.820513
18 VAL SER GLN ASN TYR PRO ILE VAL GLN ASN 0.483444 0.941176
19 ALA ASN SER ARG TYR PRO THR SER ILE ILE 0.481013 0.890411
20 SER ILE TYR PHE TPO PRO GLU LEU TYR ASP 0.47929 0.88
21 GLN MET PRO THR GLU ASP GLU TYR 0.477419 0.847222
22 GLY TYR GLN ASP TYR GLU PRO GLU ALA 0.471429 0.835821
23 TYR LEU GLU PRO ALA PRO VAL THR ALA 0.470199 0.871429
24 GLU SER ASP PRO ILE VAL ALA GLN TYR 0.46875 0.941176
25 LYS PRO ILE VAL GLN TYR ASP ASN PHE 0.466667 0.942029
26 ASN GLY TYR GLU ASN PRO THR TYR LYS 0.462963 0.926471
27 SER LEU TYR ASN THR ILE ALA THR LEU 0.461538 0.735294
28 TYR TYR SER ILE ILE PRO HIS SER ILE 0.461538 0.942857
29 ALA ASN SER ARG PHE PRO THR SER ILE ILE 0.457317 0.849315
30 PRO SER ILE ASP ARG SER THR LYS PRO 0.45625 0.810811
31 PHE ASN PHE PRO GLN ILE THR 0.453333 0.925373
32 ACE TYR PRO ILE GLN GLU THR 0.453333 0.867647
33 GLU VAL PTR GLU SER PRO 0.452055 0.813333
34 GLY TYR GLU ASN PRO THR TYR LYS PHE PHE 0.451807 0.926471
35 ARG VAL SER PRO SER THR SER TYR THR PRO 0.450704 0.867647
36 ILE THR ASP GLN VAL PRO PHE SER VAL 0.45 0.897059
37 SER PHE PHE GLU ASP ASN PHE VAL PRO GLU 0.449664 0.911765
38 TYR LEU GLU PRO GLY PRO VAL THR ALA 0.449367 0.898551
39 ILE PRO ALA TYR GLY VAL LEU THR ILE 0.449367 0.911765
40 TYR LEU GLU PRO GLY PRO VAL THR VAL 0.449367 0.898551
41 GLN VAL PRO SER ASP PRO TYR ASN TYR 0.448052 0.913043
42 LEU PRO SER PHE GLU THR ALA LEU 0.448052 0.882353
43 SER LEU ASN TYR ILE ILE LYS VAL LYS GLU 0.445161 0.782609
44 ALA ASN SER ARG ALY PRO THR SER ILE ILE 0.445122 0.789474
45 LEU PRO PHE ASP LYS SER THR ILE MET 0.443787 0.835616
46 ASP PHE GLU GLU ILE PRO GLY GLU TYR LEU 0.443114 0.898551
47 TRP GLU TYR ILE PRO ASN VAL 0.443114 0.887324
48 GLY PHE GLU PRO 0.44186 0.746269
49 ARG ILE PRO SER TYR ARG TYR ARG TYR 0.441558 0.864865
50 LYS GLN GLU PRO GLN GLU ILE ASP PHE 0.438272 0.808824
51 LYS LEU TYR GLN ASN PRO THR THR TYR ILE 0.437126 0.942029
52 ASP TYR ASN PRO TYR LEU LEU PHE LEU LYS 0.436709 0.927536
53 ALA PRO SER PTR VAL ASN VAL GLN ASN 0.436709 0.828947
54 ACE ILE GLU PRO ASJ 0.43609 0.80597
55 ALA PRO GLN PRO ALA PRO GLU ASN ALA TYR 0.435897 0.869565
56 GLU PHE SER PRO 0.435115 0.80597
57 N7P THR SEP PRO SER TYR SET 0.434211 0.779221
58 SER GLN TYR TYR TYR ASN SER LEU 0.433824 0.764706
59 TYR PRO ASN VAL ASN ILE HIS ASN PHE 0.433735 0.901408
60 ARG LEU TYR GLN ASN PRO THR THR TYR ILE 0.432749 0.866667
61 TYR TYR SER ILE ALA PRO HIS SER ILE 0.432099 0.915493
62 ALA ILE ALA TYR PHE ILE PRO ASP GLN ALA 0.431507 0.865672
63 LEU PRO PRO LEU ASP ILE THR PRO TYR 0.43125 0.884058
64 ACE ILE TYR GLU SER LEU 0.42963 0.705882
65 LYS TYR TYR SER ILE ILE PRO HIS SER ILE 0.428571 0.942857
66 ACE GLN PM3 GLU GLU ILE PRO 0.428571 0.72973
67 FME TYR PHE ILE ASN ILE LEU THR LEU 0.428571 0.708333
68 GLY ARG PRO ARG THR THR SER PHE ALA GLU 0.428571 0.797297
69 SER SER TYR ARG ARG PRO VAL GLY ILE 0.426829 0.84
70 GLU THR PHE TYR VAL ASP GLY 0.426573 0.75
71 ASN TYR THR PRO GLY PRO GLY ILE ARG PHE 0.426136 0.891892
72 LYS LEU PRO ALA GLN PHE TYR ILE LEU 0.426035 0.884058
73 SER PRO ILE VAL PRO SER PHE ASP MET 0.425926 0.835616
74 PHE GLU ALA ILE PRO ALA GLU TYR LEU 0.425926 0.882353
75 VAL TYR ILE HIS PRO PHE 0.425676 0.816901
76 SER LEU TYR ASN THR VAL ALA THR LEU 0.424658 0.705882
77 ALA SER ASN GLU ASN ILE GLU THR MET 0.42446 0.661972
78 VAL SER PHE ASN FRD PRO GLN ILE THR ALA 0.424242 0.913043
79 THR LYS ASN TYR LYS GLN THR SER VAL 0.423841 0.753623
80 ARG THR PHE SER PRO THR TYR GLY LEU 0.422619 0.878378
81 SER LEU TYR ASN VAL VAL ALA THR LEU 0.421769 0.705882
82 ALA ASN SER ARG ALA PRO THR SER ILE ILE 0.421384 0.810811
83 TYR PRO TYR ASP VAL PRO ASP TYR ALA 0.42 0.869565
84 LEU PRO PHE ASP LYS THR THR ILE MET 0.419162 0.821918
85 TYR SEP PRO THR SEP PRO SER 0.417808 0.8
86 PRO SER TYR SEP PRO THR SEP PRO SER 0.416667 0.8
87 GLU ALA ASP PRO THR GLY HIS SER TYR 0.416185 0.914286
88 VAL PRO LEU ARG PRO MET THR TYR 0.415663 0.772152
89 LEU PRO PHE ASP ARG THR THR ILE MET 0.415205 0.759494
90 TYR GLN PHE GLY PRO ASP PHE PRO ILE ALA 0.415205 0.926471
91 DTY ILE ARG LEU LPD 0.413333 0.77027
92 ALA GLU THR PHE TYR VAL ASP GLY 0.412587 0.691176
93 ASP GLY PTR MET PRO 0.412162 0.74359
94 ASP VAL GLN THR GLY ARG ARG PRO TYR GLU 0.411765 0.813333
95 ASP PHE GLU GLU ILE PRO GLU GLU TYS 0.411043 0.73494
96 SER ILE ILE ASN PHE GLU LYS LEU 0.410596 0.735294
97 LEU ALA ILE TYR SER 0.410448 0.661765
98 PHE GLN PRO GLN ASN GLY GLN PHE ILE 0.409938 0.867647
99 GLU TYR LEU GLY LEU ASP VAL PRO VAL 0.409938 0.867647
100 ALA VAL ALA PHE TYR ILE PRO ASP GLN ALA 0.409396 0.852941
101 ALA ARG THR GLU LEU TYR ARG SER LEU 0.409091 0.68
102 ASN ASP THR SER GLN THR SER SER PRO SER OPE 0.408537 0.786667
103 SER SER LEU GLU ASN PHE ALA ALA TYR VAL 0.407643 0.764706
104 GLN ASN GLY PTR VAL ASN PRO THR TYR 0.40625 0.853333
105 ASP ALA ASP GLU TYR LEU 0.405797 0.647059
106 ALA GLN ASP ILE TYR ARG ALA SER TYR 0.404908 0.739726
107 ALA ILE MET PRO ALA ARG PHE TYR PRO LYS 0.404372 0.782051
108 PRO PRO ARG PRO ILE TYR ASN ARG ASN 0.403614 0.837838
109 GLN VAL PRO LEU ARG PRO MET THR TYR LYS 0.402174 0.78481
110 ASP PHE GLU ASP TYR GLU PHE ASP 0.40146 0.652174
111 TYR MET PHE PRO ASN ALA PRO TYR LEU 0.401198 0.851351
112 ASP PHE GLU GLU ILE PRO GLY GLU TYS LEU 0.401163 0.738095
113 ASN TYR THR PRO GLY PRO GLY THR ARG PHE 0.40113 0.864865
114 SER THR SEP PRO THR PHE ASN LYS 0.4 0.786667
115 THR ASN GLU PHE TYR ALA 0.4 0.716418
116 ASN ASP LYS TYR GLU PRO PHE TRP GLU 0.4 0.871429
Similar Ligands (3D)
Ligand no: 1; Ligand: ASP ILE ASN TYR TYR THR SER GLU PRO; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader) APoc FAQ
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