Receptor
PDB id Resolution Class Description Source Keywords
5IVX 2.1 Å NON-ENZYME: IMMUNE CRYSTAL STRUCTURE OF B4.2.3 T-CELL RECEPTOR AND H2-DD P18-I1 MUS MUSCULUS MAJOR HISTOMPATIBILITY COMPLEX CLASS I MHC-I H2-DD H-2DDRECEPTOR TCR B4.2.3 B423 IMMUNE RESPONSE VIRAL IMMUNOEIMMUNE SYSTEM HUMAN IMMUNODEFICIENCY VIRUS MOLECULAR RECO
Ref.: AN ALLOSTERIC SITE IN THE T-CELL RECEPTOR C BETA DO PLAYS A CRITICAL SIGNALLING ROLE. NAT COMMUN V. 8 15260 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO B:101;
A:301;
A:302;
E:201;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
ARG GLY PRO GLY ARG ALA PHE VAL THR ILE P:1;
 Valid;
 none;
 Kd ~ 0.54 uM
1060.29 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5IVX 2.1 Å NON-ENZYME: IMMUNE CRYSTAL STRUCTURE OF B4.2.3 T-CELL RECEPTOR AND H2-DD P18-I1 MUS MUSCULUS MAJOR HISTOMPATIBILITY COMPLEX CLASS I MHC-I H2-DD H-2DDRECEPTOR TCR B4.2.3 B423 IMMUNE RESPONSE VIRAL IMMUNOEIMMUNE SYSTEM HUMAN IMMUNODEFICIENCY VIRUS MOLECULAR RECO
Ref.: AN ALLOSTERIC SITE IN THE T-CELL RECEPTOR C BETA DO PLAYS A CRITICAL SIGNALLING ROLE. NAT COMMUN V. 8 15260 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 225 families.
1 5IVX Kd ~ 0.54 uM ARG GLY PRO GLY ARG ALA PHE VAL THR ILE n/a n/a
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 67 families.
1 5IVX Kd ~ 0.54 uM ARG GLY PRO GLY ARG ALA PHE VAL THR ILE n/a n/a
2 2JCC - ALA LEU TRP GLY PHE PHE PRO VAL LEU n/a n/a
3 2UWE - ALA LEU TRP GLY PHE PHE PRO VAL LEU n/a n/a
4 1LP9 - ALA LEU TRP GLY PHE PHE PRO VAL LEU n/a n/a
5 1MWA - GLU GLN TYR LYS PHE TYR SER VAL n/a n/a
50% Homology Family (50)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 45 families.
1 6ULN - GLY ALA ASP GLY VAL GLY LYS SER ALA n/a n/a
2 2F53 - SER LEU LEU MET TRP ILE THR GLN CYS n/a n/a
3 2P5E - SER LEU LEU MET TRP ILE THR GLN CYS n/a n/a
4 2BNQ Kd = 5 uM SER LEU LEU MET TRP ILE THR GLN VAL n/a n/a
5 2BNR Kd = 13.3 uM SER LEU LEU MET TRP ILE THR GLN CYS n/a n/a
6 2PYE - SER LEU LEU MET TRP ILE THR GLN CYS n/a n/a
7 2P5W - SER LEU LEU MET TRP ILE THR GLN CYS n/a n/a
8 3VXM - ARG PHE PRO LEU THR PHE GLY TRP CYS PHE n/a n/a
9 5JZI - LYS LEU VAL ALA LEU GLY ILE ASN ALA VAL n/a n/a
10 5HHM - GLY ILE LEU GLY LEU VAL PHE THR LEU n/a n/a
11 2VLK - GLY ILE LEU GLY PHE VAL PHE THR LEU n/a n/a
12 2VLJ - GLY ILE LEU GLY PHE VAL PHE THR LEU n/a n/a
13 1OGA - GLY ILE LEU GLY PHE VAL PHE THR LEU n/a n/a
14 2VLR - GLY ILE LEU GLY PHE VAL PHE THR LEU n/a n/a
15 5ISZ Kd = 27 nM GLY ILE LEU GLY PHE VAL PHE THR LEU n/a n/a
16 3QFJ - LEU LEU PHE GLY PHE PRO VAL TYR VAL n/a n/a
17 5IVX Kd ~ 0.54 uM ARG GLY PRO GLY ARG ALA PHE VAL THR ILE n/a n/a
18 5EU6 - TYR LEU GLU PRO GLY PRO VAL THR VAL n/a n/a
19 1BD2 - LEU LEU PHE GLY TYR PRO VAL TYR VAL n/a n/a
20 6BJ8 - VAL PRO LEU THR GLU ASP ALA GLU LEU n/a n/a
21 6BJ3 Kd = 17 uM ILE PRO LEU THR GLU GLU ALA GLU LEU n/a n/a
22 5JHD Kd = 37 nM GLY ILE LEU GLY PHE VAL PHE THR LEU n/a n/a
23 2JCC - ALA LEU TRP GLY PHE PHE PRO VAL LEU n/a n/a
24 2UWE - ALA LEU TRP GLY PHE PHE PRO VAL LEU n/a n/a
25 1LP9 - ALA LEU TRP GLY PHE PHE PRO VAL LEU n/a n/a
26 5C09 - TYR LEU GLY GLY PRO ASP PHE PRO THR ILE n/a n/a
27 5C0A - MET VAL TRP GLY PRO ASP PRO LEU TYR VAL n/a n/a
28 5C08 - ARG GLN TRP GLY PRO ASP PRO ALA ALA VAL n/a n/a
29 5C0B - ARG GLN PHE GLY PRO ASP PHE PRO THR ILE n/a n/a
30 5C07 - TYR GLN PHE GLY PRO ASP PHE PRO ILE ALA n/a n/a
31 5C0C - ARG GLN PHE GLY PRO ASP TRP ILE VAL ALA n/a n/a
32 6TMO Kd = 0.75 nM GLU ALA ALA GLY ILE GLY ILE LEU THR VAL n/a n/a
33 4JFF Kd = 600 pM GLU LEU ALA GLY ILE GLY ILE LEU THR VAL n/a n/a
34 4JFD Kd = 36 uM GLU LEU ALA ALA ILE GLY ILE LEU THR VAL n/a n/a
35 5BS0 Kd = 76.7 nM GLU SER ASP PRO ILE VAL ALA GLN TYR n/a n/a
36 6D78 - ALA ALA GLY ILE GLY ILE LEU THR VAL n/a n/a
37 3QDJ - ALA ALA GLY ILE GLY ILE LEU THR VAL n/a n/a
38 1MI5 Kd ~ 10 uM PHE LEU ARG GLY ARG ALA TYR GLY LEU n/a n/a
39 3VXS - ARG TYR PRO LEU THR LEU GLY TRP CYS PHE n/a n/a
40 3VXR - ARG TYR PRO LEU THR PHE GLY TRP CYS PHE n/a n/a
41 1MWA - GLU GLN TYR LYS PHE TYR SER VAL n/a n/a
42 4G9F - LYS ARG TRP ILE ILE MET GLY LEU ASN LYS n/a n/a
43 4G8G - LYS ARG TRP ILE ILE LEU GLY LEU ASN LYS n/a n/a
44 6VRN - HIS MET THR GLU VAL VAL ARG HIS CYS n/a n/a
45 6PVD Kd = 200 uM N18 C9 H11 N3 O5 COC(=O)CCN....
46 4NQD - 2LJ C12 H20 N4 O6 CC/C=N/C1=....
47 4LCW - 1VY C12 H16 N4 O7 CC1=C(N(C2....
48 4L4V Kd = 1.65 uM 1VY C12 H16 N4 O7 CC1=C(N(C2....
49 6PVC Kd = 172 uM P1J C8 H9 N3 O5 C1=C(NC(=O....
50 6RPB - SER LEU LEU MET TRP ILE THR GLN VAL n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: ARG GLY PRO GLY ARG ALA PHE VAL THR ILE; Similar ligands found: 73
No: Ligand ECFP6 Tc MDL keys Tc
1 ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 1 1
2 ARG GLY PRO GLY CYS ALA PHE VAL THR ILE 0.804054 0.956522
3 ILE GLY PRO GLY ARG ALA PHE TYR THR ILE 0.691824 0.876712
4 ILE GLY PRO GLY ARG ALA PHE TYR THR 0.690323 0.849315
5 ILE GLY PRO GLY ARG ALA PHE TYR VAL 0.679487 0.849315
6 ILE GLY PRO GLY ARG ALA PHE TYR ALA 0.653846 0.835616
7 ASN TYR THR PRO GLY PRO GLY THR ARG PHE 0.54023 0.864865
8 ASN TYR THR PRO GLY PRO GLY ILE ARG PHE 0.539773 0.891892
9 ARG GLN PHE GLY PRO ASP PHE PRO THR ILE 0.494444 0.929577
10 GLY ARG PRO ARG THR THR SER PHE ALA GLU 0.485714 0.927536
11 ALA PHE ARG ILE PRO LEU THR ARG 0.485207 0.970588
12 ARG THR PHE SER PRO THR TYR GLY LEU 0.48 0.878378
13 ARG PRO GLY ASN PHE LEU GLN SER ARG LEU 0.478022 0.942029
14 ARG GLN PHE GLY PRO ASP TRP ILE VAL ALA 0.476923 0.849315
15 LEU PRO PHE GLU ARG ALA THR VAL MET 0.475138 0.902778
16 ARG SEP PRO VAL PHE SER 0.473373 0.824324
17 PHE LEU TRP GLY PRO ARG ALA LEU VAL 0.472826 0.821918
18 ARG LEU TYR GLN ASN PRO THR THR TYR ILE 0.472222 0.917808
19 PHE LEU ARG GLY ARG ALA TYR VAL LEU 0.470238 0.69863
20 ARG PRO GLY ASN PHE LEU GLN SER ARG PRO 0.463687 0.928571
21 ARG PRO PRO GLY PHE SER PRO PHE ALA 0.462428 0.859155
22 ARG PRO MET THR PHE LYS GLY ALA LEU 0.454545 0.890411
23 LEU PRO PHE GLU ARG ALA THR ILE MET 0.454054 0.916667
24 ARG GLY PHE ALA LEU M3L SER THR HIS GLY 0.453552 0.807692
25 ARG ABA VAL ILE PHE ALA ASN ILE 0.453416 0.724638
26 ARG TYR GLY PHE VAL ALA ASN PHE 0.451807 0.689189
27 SER SER TYR ARG ARG PRO VAL GLY ILE 0.451429 0.943662
28 ARG ILE PRO SER TYR ARG TYR ARG TYR 0.449102 0.890411
29 ARG ARG LEU PRO ILE PHE SER ARG LEU 0.448276 0.942029
30 ARG PHE PRO LEU THR PHE GLY TRP 0.446809 0.890411
31 GLU GLU PHE GLY ARG ALA PHE SER PHE 0.442424 0.690141
32 DPN PRO DAR DTH NH2 0.441558 0.895522
33 VAL MET ALA PRO ARG THR LEU PHE LEU 0.438889 0.876712
34 ALA VAL ALA PHE TYR ILE PRO ASP GLN ALA 0.4375 0.75
35 ARG VAL ALA SER PRO THR SER GLY VAL 0.436364 0.898551
36 ASP PHE GLU GLU ILE PRO GLY GLU PTR 0.431694 0.734177
37 ARG TYR PRO LEU THR PHE GLY TRP CYS PHE 0.431373 0.88
38 ALA ASN SER ARG PHE PRO THR SER ILE ILE 0.430939 0.928571
39 ARG TYR PRO LEU THR PHE GLY TRP 0.430769 0.866667
40 ARG PRO PRO GLY PHE 0.43038 0.823529
41 ARG PRO PRO GLY PHE SER PRO PHE ARG 0.43038 0.823529
42 ARG THR TYR SEP GLY PRO MET ASN LYS VAL 0.427136 0.795181
43 ACE GLY PHE GLY VAL VAL PRO SER PHE TYR 0.426829 0.785714
44 ARG ABA PHE ILE PHE ALA ASN ILE 0.425926 0.690141
45 THR PRO ARG VAL THR GLY GLY GLY ALA MET 0.425287 0.876712
46 ARG PHE PRO LEU THR PHE GLY TRP CYS PHE 0.425 0.891892
47 ILE ARG TYR PRO LYS THR PHE GLY TRP 0.423645 0.866667
48 DPN PRO DAR ILE NH2 0.423077 0.850746
49 GLU THR VAL ARG PHE GLN SER ASP 0.422619 0.73913
50 ARG PRO PRO ILE PHE ILE ARG ARG LEU 0.420455 0.884058
51 ILE ARG ALA ALA PRO PRO PRO LEU PHE 0.420455 0.871429
52 ARG ILE PHE SER 0.42 0.705882
53 ASP PHE GLU GLU ILE PRO GLY GLU TYR LEU 0.418478 0.794521
54 ARG VAL ALA SEP PRO THR SER GLY VAL 0.417143 0.826667
55 LEU PRO PHE ASP ARG THR THR ILE MET 0.416216 0.930556
56 MET CYS PRO ARG MET THR ALA VAL MET 0.412429 0.875
57 ASN ARG PRO VAL TYR ILE PRO ARG PRO PRO 0.412429 0.9
58 PHE LEU ARG GLY ARG ALA TYR GLY LEU 0.410714 0.69863
59 LEU PRO PHE GLU LEU ARG GLY HIS LEU VAL 0.410526 0.833333
60 ALA LEU MET PRO GLY GLN PHE PHE VAL 0.409091 0.716216
61 GLU ARG THR ILE PRO ILE THR ARG GLU 0.408537 0.940298
62 VAL ALA PHE ARG SER 0.407895 0.691176
63 ARG PRO MET THR TYR LYS GLY ALA LEU 0.407216 0.855263
64 ALA ILE MET PRO ALA ARG PHE TYR PRO LYS 0.406091 0.805195
65 ARG TYR PRO LEU THR LEU GLY TRP CYS PHE 0.405797 0.868421
66 LEU LEU PHE GLY LYS PRO VAL TYR VAL 0.405556 0.756757
67 ALA ILE ALA TYR PHE ILE PRO ASP GLN ALA 0.404908 0.736111
68 ARG ARG ALA SEP ALA PRO LEU PRO 0.404624 0.789474
69 DPN PRO DAR CYS NH2 0.403846 0.794118
70 ILE SER PRO ARG THR LEU ASP ALA TRP 0.40201 0.917808
71 ALA THR ARG ASN PHE SER GLY 0.401235 0.753623
72 GLY ARG PHE ALA ALA ALA ILE ALA LYS 0.4 0.735294
73 ILE LEU GLY PRO PRO GLY SER VAL TYR 0.4 0.847222
Similar Ligands (3D)
Ligand no: 1; Ligand: ARG GLY PRO GLY ARG ALA PHE VAL THR ILE; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5IVX; Ligand: ARG GLY PRO GLY ARG ALA PHE VAL THR ILE; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5ivx.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
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