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 1443 families.
1 5YD4 Kd = 13 uM ASP ILE ASN TYR TYR ALA SER GLU PRO n/a n/a
2 5YY4 Kd = 98 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 1205 families.
1 5YD4 Kd = 13 uM ASP ILE ASN TYR TYR ALA SER GLU PRO n/a n/a
2 5YY4 Kd = 98 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 - TRE C12 H22 O11 C([C@@H]1[....
50% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 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 = 98 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 4H0I - MMA C7 H14 O6 CO[C@@H]1[....
9 5VF2 - TRE C12 H22 O11 C([C@@H]1[....
10 5J75 Ki = 0.63 nM 6GQ C19 H24 N4 O3 S Cc1ccc(cc1....
11 5A2K - ALA PRO ASP THR ARG PRO A2G n/a n/a
12 5A2L - ALA PRO ASP CYS ARG PRO A2G n/a n/a
13 5A2I - ALA PRO ASP SER ARG PRO A2G n/a n/a
14 5A2J - ALA PRO ASP THR ARG PRO n/a n/a
15 5FXC - ALA PRO ASP THR ARG PRO n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ASP ILE ASN TYR TYR ALA SER GLU PRO; Similar ligands found: 116
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 0.716535 0.985075
4 ASP ILE ASN TYS TYS THR SER GLU PRO 0.618705 0.817073
5 ILE SER TYR GLY ASN ASP ALA LEU MET PRO 0.588235 0.902778
6 ASP TYR GLU PRO ILE PRO GLU GLU ALA PHE 0.569536 0.911765
7 GLY TYR GLN ASP TYR GLU PRO GLU ALA 0.559702 0.835821
8 GLU SER ASP PRO ILE VAL ALA GLN TYR 0.532468 0.941176
9 PHE TYR ALA PRO GLU PRO ILE THR SER LEU 0.518987 0.942857
10 GLN ASN TYR PRO ILE VAL GLN 0.510345 0.897059
11 THR PRO TYR ASP ILE ASN GLN MET LEU 0.506329 0.875
12 ALA PRO GLN PRO ALA PRO GLU ASN ALA TYR 0.5 0.869565
13 PHE GLU ALA ILE PRO ALA GLU TYR LEU 0.496774 0.882353
14 VAL SER GLN ASN TYR PRO ILE VAL GLN ASN 0.490066 0.941176
15 LEU ASN PHE PRO ILE SER PRO 0.485915 0.898551
16 SER ILE TYR PHE TPO PRO GLU LEU TYR ASP 0.485207 0.88
17 SER SER LEU GLU ASN PHE ALA ALA TYR VAL 0.48 0.764706
18 ASP ALA ASP GLU TYR LEU 0.477273 0.647059
19 LYS PRO ILE VAL GLN TYR ASP ASN PHE 0.472727 0.942029
20 GLU GLU PRO THR VAL ILE LYS LYS TYR 0.465839 0.898551
21 ACE GLN PM3 GLU GLU ILE PRO 0.465278 0.72973
22 ALA GLN ASP ILE TYR ARG ALA SER TYR 0.464968 0.739726
23 ALA ASN SER ARG TYR PRO THR SER ILE ILE 0.462963 0.890411
24 LEU ALA ILE TYR SER 0.461538 0.661765
25 SER ASP PTR MET ASN MET THR PRO 0.461538 0.820513
26 LEU TYR ALA SER PRO GLN LEU GLU GLY PHE 0.461078 0.926471
27 LYS TYR TYR SER ILE ILE PRO HIS SER ILE 0.458599 0.942857
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 ASP PHE GLU GLU ILE PRO GLY GLU TYR LEU 0.449102 0.898551
36 GLU VAL PTR GLU SER PRO 0.44898 0.813333
37 SER LEU TYR ASN THR ILE ALA THR LEU 0.448276 0.735294
38 TYR LEU GLU PRO ALA PRO VAL THR ALA 0.448052 0.871429
39 ACE LEU TYR ALA SER SER ASN PRO ALA PTR 0.447205 0.868421
40 HIS SER ILE THR TYR LEU LEU PRO VAL 0.445783 0.915493
41 GLN VAL PRO SER ASP PRO TYR ASN TYR 0.445161 0.913043
42 LYS GLN GLU PRO GLN GLU ILE ASP PHE 0.444444 0.808824
43 SER GLN TYR TYR TYR ASN SER LEU 0.441176 0.764706
44 ACE TYR PRO ILE GLN GLU THR 0.440789 0.867647
45 TRP GLU TYR ILE PRO ASN VAL 0.440476 0.887324
46 GLY PHE GLU PRO 0.438462 0.746269
47 TYR TYR SER ILE ALA PRO HIS SER ILE 0.438272 0.915493
48 TYR GLN PHE GLY PRO ASP PHE PRO ILE ALA 0.43787 0.926471
49 GLN MET PRO THR GLU ASP GLU TYR 0.4375 0.847222
50 SER PHE PHE GLU ASP ASN PHE VAL PRO GLU 0.437086 0.911765
51 ACE ILE TYR GLU SER LEU 0.437037 0.705882
52 GLY ASN TYR SER PHE TYR ALA LEU 0.435714 0.764706
53 ALA VAL ALA PHE TYR ILE PRO ASP GLN ALA 0.435374 0.852941
54 GLY ARG PRO ARG THR THR SER PHE ALA GLU 0.434524 0.797297
55 ASP ARG VAL TYR ILE HIS PRO PHE 0.433566 0.828571
56 ALA ILE MET PRO ALA ARG PHE TYR PRO LYS 0.433333 0.782051
57 SER SER TYR ARG ARG PRO VAL GLY ILE 0.432927 0.84
58 ACE ILE GLU PRO ASJ 0.432836 0.80597
59 GLU PHE SER PRO 0.431818 0.80597
60 TYR PRO ASN VAL ASN ILE HIS ASN PHE 0.431138 0.901408
61 GLU ALA ASP PRO THR GLY HIS SER TYR 0.430233 0.914286
62 TYR LEU GLU PRO GLY PRO VAL THR ALA 0.428571 0.898551
63 TYR LEU GLU PRO GLY PRO VAL THR VAL 0.428571 0.898551
64 ILE PRO ALA TYR GLY VAL LEU THR ILE 0.428571 0.911765
65 ASP PHE GLU GLU ILE PRO GLU GLU TYS 0.425926 0.73494
66 SER SER LEU GLU ASN PHE ARG ALA TYR VAL 0.42515 0.72973
67 ASN GLY TYR GLU ASN PRO THR TYR LYS 0.42515 0.926471
68 TYR MET PHE PRO ASN ALA PRO TYR LEU 0.424242 0.851351
69 GLY TYR GLU ASN PRO THR TYR LYS PHE PHE 0.423529 0.926471
70 SER PRO ILE VAL PRO SER PHE ASP MET 0.423313 0.835616
71 THR ASN GLU TYR TYR VAL 0.423077 0.676471
72 PHE ASN PHE PRO GLN ILE THR 0.422078 0.925373
73 DTY ILE ARG LEU LPD 0.42 0.77027
74 LEU PRO PRO LEU ASP ILE THR PRO TYR 0.419753 0.884058
75 DVA DPR GLY DSN DGN DHI DTY DAS DSN 0.419162 0.901408
76 VAL ASN ASP ILE PHE GLU ALA ILE 0.418919 0.632353
77 THR ASN GLU PHE TYR ALA 0.417266 0.716418
78 TYR PRO TYR ASP VAL PRO ASP TYR ALA 0.417219 0.869565
79 SER ILE ILE ASN PHE GLU LYS LEU 0.417219 0.735294
80 ALA PRO SER PTR VAL ASN VAL GLN ASN 0.416149 0.828947
81 GLU TYR LEU GLY LEU ASP VAL PRO VAL 0.416149 0.867647
82 LEU PRO PHE GLU ARG ALA THR ILE MET 0.412429 0.746835
83 SER LEU TYR ASN THR VAL ALA THR LEU 0.412162 0.705882
84 ALA ALA SER LEU TYR GLU LYS LYS ALA ALA 0.412162 0.73913
85 PHE ALA PRO GLY ASN TYR PRO ALA LEU 0.409639 0.914286
86 PRO SER ILE ASP ARG SER THR LYS PRO 0.409639 0.810811
87 SER LEU TYR ASN VAL VAL ALA THR LEU 0.409396 0.705882
88 ASP PHE GLU ASP TYR GLU PHE ASP 0.408759 0.652174
89 LEU PRO PHE ASP LYS SER THR ILE MET 0.408046 0.835616
90 SER SER ILE GLU PHE ALA ARG LEU 0.407643 0.648649
91 PHE GLN PRO GLN ASN GLY GLN PHE ILE 0.407407 0.867647
92 ASP PHE GLU GLU ILE PRO GLY GLU TYS LEU 0.406977 0.738095
93 ILE GLY PRO GLY ARG ALA PHE TYR ALA 0.405882 0.835616
94 TYR LEU LYS GLU PRO VAL HIS GLY VAL 0.405714 0.84507
95 GLU LEU ASP LYS TYR ALA SER 0.405405 0.75
96 ASN ASP LYS TYR GLU PRO PHE TRP GLU 0.405405 0.871429
97 ASN ARG PRO VAL TYR ILE PRO ARG PRO PRO 0.404908 0.773333
98 LYS GLN TRP ASP ASN TYR GLU PHE ILE TRP 0.404762 0.757143
99 ILE GLY PRO GLY ARG ALA PHE TYR THR 0.404624 0.849315
100 ILE GLY PRO GLY ARG ALA PHE TYR VAL 0.404624 0.824324
101 ILE GLY PRO GLY ARG ALA PHE TYR THR ILE 0.404494 0.876712
102 ALA LEU TYR ASN THR ALA ALA ALA LEU 0.404255 0.661765
103 VAL TYR ILE HIS PRO PHE 0.403974 0.816901
104 ALA ASN SER ARG PHE PRO THR SER ILE ILE 0.403509 0.849315
105 ASN PHE ASP ASN PRO VAL TYR ARG LYS THR 0.403315 0.853333
106 ALA VAL TYR ASN PHE ALA THR MET 0.401316 0.680556
107 GLU ILE ILE ASN PHE GLU LYS LEU 0.401316 0.666667
108 ASN ARG PRO VAL TYR ILE PRO PRO PRO PRO 0.401316 0.84058
109 SER ASP ILE LEU PHE PRO ALA ASP SER 0.401274 0.882353
110 PRO PRO ARG PRO ILE TYR ASN ARG ASN 0.401198 0.837838
111 LYS LEU TYR GLN ASN PRO THR THR TYR ILE 0.401163 0.942029
112 ARG MET PHE PRO ASN ALA PRO TYR LEU 0.40113 0.8
113 ASN ASP TRP LEU LEU PRO SER TYR 0.4 0.929577
114 ASN TYR THR PRO GLY PRO GLY ILE ARG PHE 0.4 0.891892
115 ASP GLY PTR MET PRO 0.4 0.74359
116 ILE PRO LEU THR GLU GLU ALA GLU LEU 0.4 0.811594
Similar Binding Sites (Proteins are less than 50% similar to leader) APoc FAQ
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