Receptor
PDB id Resolution Class Description Source Keywords
5YD4 1.35 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE SCFV ANTIBODY 4B08 WITH EPITOPE PEP (MUTATION T6A) 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;
C:303;
A:301;
E:301;
E:302;
C:302;
C:301;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
 submit data
96.063 O4 S [O-]S...
ASP ILE ASN TYR TYR ALA SER GLU PRO F:1;
D:2;
H:3;
B:2;
 Valid;
Valid;
Valid;
Valid;
 none;
Atoms found LESS than expected: % Diff = 0.105;
Atoms found LESS than expected: % Diff = 0.211;
Atoms found LESS than expected: % Diff = 0.105;
 Kd = 13 uM
1069.09 n/a O=C(N...
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 ALA SER GLU PRO; Similar ligands found: 119
No: Ligand ECFP6 Tc MDL keys Tc
1 ASP ILE ASN TYR TYR ALA SER GLU PRO 1 1
2 ASP ILE ASN TYR TYR THR SER GLU PRO 0.860656 1
3 ASP ILE ALA TYR TYR THR SER GLU PRO 0.684615 0.985075
4 ASP TYR ILE ASN THR ASN VAL LEU PRO 0.615942 0.926471
5 ASP ILE ASN TYS TYS THR SER GLU PRO 0.595745 0.817073
6 ILE SER TYR GLY ASN ASP ALA LEU MET PRO 0.588235 0.902778
7 ASP TYR GLU PRO ILE PRO GLU GLU ALA PHE 0.569536 0.911765
8 GLN ILE MET TYR ASN TYR PRO ALA MET 0.562914 0.875
9 ASP PHE ALA ASN THR PHE LEU PRO 0.542253 0.911765
10 GLU SER ASP PRO ILE VAL ALA GLN TYR 0.532468 0.941176
11 PHE TYR ALA PRO GLU PRO ILE THR SER LEU 0.518987 0.942857
12 GLN ASN TYR PRO ILE VAL GLN 0.510345 0.897059
13 THR PRO TYR ASP ILE ASN GLN MET LEU 0.506329 0.875
14 ALA PRO GLN PRO ALA PRO GLU ASN ALA TYR 0.5 0.869565
15 PHE GLU ALA ILE PRO ALA GLU TYR LEU 0.496774 0.882353
16 VAL SER GLN ASN TYR PRO ILE VAL GLN ASN 0.490066 0.941176
17 GLY TYR GLN ASP TYR GLU PRO GLU ALA 0.489209 0.835821
18 LEU ASN PHE PRO ILE SER PRO 0.485915 0.898551
19 SER ILE TYR PHE TPO PRO GLU LEU TYR ASP 0.485207 0.88
20 SER SER LEU GLU ASN PHE ALA ALA TYR VAL 0.48 0.764706
21 ASP ALA ASP GLU TYR LEU 0.477273 0.647059
22 LYS PRO ILE VAL GLN TYR ASP ASN PHE 0.472727 0.942029
23 GLU GLU PRO THR VAL ILE LYS LYS TYR 0.465839 0.898551
24 ALA GLN ASP ILE TYR ARG ALA SER TYR 0.464968 0.739726
25 SER ASP PTR MET ASN MET THR PRO 0.461538 0.820513
26 LEU ALA ILE TYR SER 0.461538 0.661765
27 LEU TYR ALA SER PRO GLN LEU GLU GLY PHE 0.461078 0.926471
28 TYR TYR SER ILE ILE PRO HIS SER ILE 0.458599 0.942857
29 ALA ILE ALA TYR PHE ILE PRO ASP GLN ALA 0.458333 0.865672
30 LYS LEU PRO ALA GLN PHE TYR ILE LEU 0.457831 0.884058
31 ARG ILE PRO SER TYR ARG TYR ARG TYR 0.457516 0.864865
32 PRO ALA ILE LEU TYR ALA LEU LEU SER SER 0.455782 0.838235
33 LEU PRO SER PHE GLU THR ALA LEU 0.454545 0.882353
34 ASP GLU LEU GLU ILE LYS ALA TYR 0.452703 0.710145
35 SER LEU ASN TYR ILE ILE LYS VAL LYS GLU 0.451613 0.782609
36 ASP PHE GLU GLU ILE PRO GLY GLU TYR LEU 0.449102 0.898551
37 GLU VAL PTR GLU SER PRO 0.44898 0.813333
38 SER LEU TYR ASN THR ILE ALA THR LEU 0.448276 0.735294
39 TYR LEU GLU PRO ALA PRO VAL THR ALA 0.448052 0.871429
40 ACE LEU TYR ALA SER SER ASN PRO ALA PTR 0.447205 0.868421
41 HIS SER ILE THR TYR LEU LEU PRO VAL 0.445783 0.915493
42 GLN VAL PRO SER ASP PRO TYR ASN TYR 0.445161 0.913043
43 LYS GLN GLU PRO GLN GLU ILE ASP PHE 0.444444 0.808824
44 ASP TYR ASN PRO TYR LEU LEU PHE LEU LYS 0.443038 0.927536
45 SER GLN TYR TYR TYR ASN SER LEU 0.441176 0.764706
46 ACE TYR PRO ILE GLN GLU THR 0.440789 0.867647
47 TRP GLU TYR ILE PRO ASN VAL 0.440476 0.887324
48 GLY PHE GLU PRO 0.438462 0.746269
49 ASP PHE GLN GLU SER ALA ASP SER PHE LEU 0.438356 0.720588
50 TYR TYR SER ILE ALA PRO HIS SER ILE 0.438272 0.915493
51 TYR GLN PHE GLY PRO ASP PHE PRO ILE ALA 0.43787 0.926471
52 GLN MET PRO THR GLU ASP GLU TYR 0.4375 0.847222
53 SER PHE PHE GLU ASP ASN PHE VAL PRO GLU 0.437086 0.911765
54 ACE ILE TYR GLU SER LEU 0.437037 0.705882
55 GLY ASN TYR SER PHE TYR ALA LEU 0.435714 0.764706
56 ALA VAL ALA PHE TYR ILE PRO ASP GLN ALA 0.435374 0.852941
57 ACE GLN PM3 GLU GLU ILE PRO 0.435374 0.72973
58 GLY ARG PRO ARG THR THR SER PHE ALA GLU 0.434524 0.797297
59 GLU PRO VAL GLU THR THR ASP TYR 0.434211 0.882353
60 ALA ILE MET PRO ALA ARG PHE TYR PRO LYS 0.433333 0.782051
61 ALA ASN SER ARG TYR PRO THR SER ILE ILE 0.432927 0.890411
62 SER SER TYR ARG ARG PRO VAL GLY ILE 0.432927 0.84
63 ACE ILE GLU PRO ASJ 0.432836 0.80597
64 GLU PHE SER PRO 0.431818 0.80597
65 TYR PRO ASN VAL ASN ILE HIS ASN PHE 0.431138 0.901408
66 GLU ALA ASP PRO THR GLY HIS SER TYR 0.430233 0.914286
67 TYR LEU GLU PRO GLY PRO VAL THR VAL 0.428571 0.898551
68 ILE PRO ALA TYR GLY VAL LEU THR ILE 0.428571 0.911765
69 TYR LEU GLU PRO GLY PRO VAL THR ALA 0.428571 0.898551
70 ASP PHE GLU GLU ILE PRO GLU GLU TYS 0.425926 0.73494
71 LYS TYR TYR SER ILE ILE PRO HIS SER ILE 0.425926 0.942857
72 SER SER LEU GLU ASN PHE ARG ALA TYR VAL 0.42515 0.72973
73 ASN GLY TYR GLU ASN PRO THR TYR LYS 0.42515 0.926471
74 TYR MET PHE PRO ASN ALA PRO TYR LEU 0.424242 0.851351
75 GLY TYR GLU ASN PRO THR TYR LYS PHE PHE 0.423529 0.926471
76 SER PRO ILE VAL PRO SER PHE ASP MET 0.423313 0.835616
77 PHE ASN PHE PRO GLN ILE THR 0.422078 0.925373
78 DTY ILE ARG LEU LPD 0.42 0.77027
79 LEU PRO PRO LEU ASP ILE THR PRO TYR 0.419753 0.884058
80 VAL ASN ASP ILE PHE GLU ALA ILE 0.418919 0.632353
81 ACE ASP PTR ALA GLU PRO MET ASP ALA NH2 0.418182 0.734177
82 LYS ARG LYS SER ARG TRP ASP GLU THR PRO 0.417582 0.802632
83 THR ASN GLU PHE TYR ALA 0.417266 0.716418
84 TYR PRO TYR ASP VAL PRO ASP TYR ALA 0.417219 0.869565
85 SER ILE ILE ASN PHE GLU LYS LEU 0.417219 0.735294
86 ALA PRO SER PTR VAL ASN VAL GLN ASN 0.416149 0.828947
87 GLU TYR LEU GLY LEU ASP VAL PRO VAL 0.416149 0.867647
88 LEU PRO PHE GLU ARG ALA THR ILE MET 0.412429 0.746835
89 SER LEU TYR ASN THR VAL ALA THR LEU 0.412162 0.705882
90 ALA ALA SER LEU TYR GLU LYS LYS ALA ALA 0.412162 0.73913
91 PHE ALA PRO GLY ASN TYR PRO ALA LEU 0.409639 0.914286
92 PRO SER ILE ASP ARG SER THR LYS PRO 0.409639 0.810811
93 SER LEU TYR ASN VAL VAL ALA THR LEU 0.409396 0.705882
94 ASP PHE GLU ASP TYR GLU PHE ASP 0.408759 0.652174
95 LEU PRO PHE ASP LYS SER THR ILE MET 0.408046 0.835616
96 SER SER ILE GLU PHE ALA ARG LEU 0.407643 0.648649
97 PHE GLN PRO GLN ASN GLY GLN PHE ILE 0.407407 0.867647
98 ASP PHE GLU GLU ILE PRO GLY GLU TYS LEU 0.406977 0.738095
99 ILE GLY PRO GLY ARG ALA PHE TYR ALA 0.405882 0.835616
100 TYR LEU LYS GLU PRO VAL HIS GLY VAL 0.405714 0.84507
101 GLU LEU ASP LYS TYR ALA SER 0.405405 0.75
102 ASN ASP LYS TYR GLU PRO PHE TRP GLU 0.405405 0.871429
103 ILE GLY PRO GLY ARG ALA PHE TYR THR 0.404624 0.849315
104 ILE GLY PRO GLY ARG ALA PHE TYR VAL 0.404624 0.824324
105 ILE GLY PRO GLY ARG ALA PHE TYR THR ILE 0.404494 0.876712
106 ALA LEU TYR ASN THR ALA ALA ALA LEU 0.404255 0.661765
107 VAL TYR ILE HIS PRO PHE 0.403974 0.816901
108 ALA ASN SER ARG PHE PRO THR SER ILE ILE 0.403509 0.849315
109 ASN ARG PRO VAL TYR ILE PRO PRO PRO PRO 0.401316 0.84058
110 GLU ILE ILE ASN PHE GLU LYS LEU 0.401316 0.666667
111 ALA VAL TYR ASN PHE ALA THR MET 0.401316 0.680556
112 PRO PRO ARG PRO ILE TYR ASN ARG ASN 0.401198 0.837838
113 LYS LEU TYR GLN ASN PRO THR THR TYR ILE 0.401163 0.942029
114 ARG MET PHE PRO ASN ALA PRO TYR LEU 0.40113 0.8
115 ILE PRO LEU THR GLU GLU ALA GLU LEU 0.4 0.811594
116 ASN TYR THR PRO GLY PRO GLY ILE ARG PHE 0.4 0.891892
117 ASN ARG PRO VAL TYR ILE PRO ARG PRO PRO 0.4 0.773333
118 ASP GLY PTR MET PRO 0.4 0.74359
119 ASN ASP TRP LEU LEU PRO SER TYR 0.4 0.929577
Similar Ligands (3D)
Ligand no: 1; Ligand: ASP ILE ASN TYR TYR ALA SER GLU PRO; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader) APoc FAQ
Feedback