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
1075.28 n/a O=C([...
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 199 families.
1 5IVX Kd ~ 0.54 uM ARG GLY PRO GLY ARG ALA PHE VAL THR ILE n/a n/a
70% Homology Family (33)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 65 families.
1 4JFF Kd = 600 pM GLU LEU ALA GLY ILE GLY ILE LEU THR VAL n/a n/a
2 4JFD Kd = 36 uM GLU LEU ALA ALA ILE GLY ILE LEU THR VAL n/a n/a
3 2F53 - SER LEU LEU MET TRP ILE THR GLN CYS n/a n/a
4 2P5E - SER LEU LEU MET TRP ILE THR GLN CYS n/a n/a
5 2BNQ Kd = 5 uM SER LEU LEU MET TRP ILE THR GLN VAL n/a n/a
6 2BNR Kd = 13.3 uM SER LEU LEU MET TRP ILE THR GLN CYS n/a n/a
7 2PYE - SER LEU LEU MET TRP ILE THR GLN CYS n/a n/a
8 2P5W - SER LEU LEU MET TRP ILE THR GLN CYS n/a n/a
9 5HHM - GLY ILE LEU GLY LEU VAL PHE THR LEU n/a n/a
10 2VLK - GLY ILE LEU GLY PHE VAL PHE THR LEU n/a n/a
11 2VLJ - GLY ILE LEU GLY PHE VAL PHE THR LEU n/a n/a
12 1OGA - GLY ILE LEU GLY PHE VAL PHE THR LEU n/a n/a
13 2VLR - GLY ILE LEU GLY PHE VAL PHE THR LEU n/a n/a
14 5ISZ Kd = 27 nM GLY ILE LEU GLY PHE VAL PHE THR LEU n/a n/a
15 3QFJ - LEU LEU PHE GLY PHE PRO VAL TYR VAL n/a n/a
16 5IVX Kd ~ 0.54 uM ARG GLY PRO GLY ARG ALA PHE VAL THR ILE n/a n/a
17 5EU6 - TYR LEU GLU PRO GLY PRO VAL THR VAL n/a n/a
18 1BD2 - LEU LEU PHE GLY TYR PRO VAL TYR VAL n/a n/a
19 5JHD Kd = 37 nM GLY ILE LEU GLY PHE VAL PHE THR LEU n/a n/a
20 2UWE - ALA LEU TRP GLY PHE PHE PRO VAL LEU n/a n/a
21 3QDJ - ALA ALA GLY ILE GLY ILE LEU THR VAL n/a n/a
22 5C09 - TYR LEU GLY GLY PRO ASP PHE PRO THR ILE n/a n/a
23 5C0A - MET VAL TRP GLY PRO ASP PRO LEU TYR VAL n/a n/a
24 5C08 - ARG GLN TRP GLY PRO ASP PRO ALA ALA VAL n/a n/a
25 5C0B - ARG GLN PHE GLY PRO ASP PHE PRO THR ILE n/a n/a
26 5C07 - TYR GLN PHE GLY PRO ASP PHE PRO ILE ALA n/a n/a
27 5C0C - ARG GLN PHE GLY PRO ASP TRP ILE VAL ALA n/a n/a
28 5BS0 Kd = 76.7 nM GLU SER ASP PRO ILE VAL ALA GLN TYR n/a n/a
29 1MI5 Kd ~ 10 uM PHE LEU ARG GLY ARG ALA TYR GLY LEU n/a n/a
30 3VXS - ARG TYR PRO LEU THR LEU GLY TRP CYS PHE n/a n/a
31 3VXR - ARG TYR PRO LEU THR PHE GLY TRP CYS PHE n/a n/a
32 4G9F - LYS ARG TRP ILE ILE MET GLY LEU ASN LYS n/a n/a
33 4G8G - LYS ARG TRP ILE ILE LEU GLY LEU ASN LYS n/a n/a
50% Homology Family (41)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 43 families.
1 4JFF Kd = 600 pM GLU LEU ALA GLY ILE GLY ILE LEU THR VAL n/a n/a
2 4JFD Kd = 36 uM GLU LEU ALA ALA ILE GLY ILE LEU THR VAL n/a n/a
3 2F53 - SER LEU LEU MET TRP ILE THR GLN CYS n/a n/a
4 2P5E - SER LEU LEU MET TRP ILE THR GLN CYS n/a n/a
5 2BNQ Kd = 5 uM SER LEU LEU MET TRP ILE THR GLN VAL n/a n/a
6 2BNR Kd = 13.3 uM SER LEU LEU MET TRP ILE THR GLN CYS n/a n/a
7 2PYE - SER LEU LEU MET TRP ILE THR GLN CYS n/a n/a
8 2P5W - SER LEU LEU MET TRP ILE THR GLN CYS n/a n/a
9 3VXM - ARG PHE PRO LEU THR PHE GLY TRP CYS PHE n/a n/a
10 5JZI - LYS LEU VAL ALA LEU GLY ILE ASN ALA VAL n/a n/a
11 5HHM - GLY ILE LEU GLY LEU VAL PHE THR LEU n/a n/a
12 2VLK - GLY ILE LEU GLY PHE VAL PHE THR LEU n/a n/a
13 2VLJ - GLY ILE LEU GLY PHE VAL PHE THR LEU n/a n/a
14 1OGA - GLY ILE LEU GLY PHE VAL PHE THR LEU n/a n/a
15 2VLR - GLY ILE LEU GLY PHE VAL PHE THR LEU n/a n/a
16 5ISZ Kd = 27 nM GLY ILE LEU GLY PHE VAL PHE THR LEU n/a n/a
17 3QFJ - LEU LEU PHE GLY PHE PRO VAL TYR VAL n/a n/a
18 5IVX Kd ~ 0.54 uM ARG GLY PRO GLY ARG ALA PHE VAL THR ILE n/a n/a
19 5EU6 - TYR LEU GLU PRO GLY PRO VAL THR VAL n/a n/a
20 1BD2 - LEU LEU PHE GLY TYR PRO VAL TYR VAL n/a n/a
21 5JHD Kd = 37 nM GLY ILE LEU GLY PHE VAL PHE THR LEU n/a n/a
22 4NQD - 2LJ C12 H18 N4 O7 CC(=O)/C=N....
23 4LCW - 1VY C12 H16 N4 O7 CC1=C(N(C2....
24 4L4V Kd = 1.65 uM 1VY C12 H16 N4 O7 CC1=C(N(C2....
25 2JCC - ALA LEU TRP GLY PHE PHE PRO VAL LEU n/a n/a
26 2UWE - ALA LEU TRP GLY PHE PHE PRO VAL LEU n/a n/a
27 1LP9 - ALA LEU TRP GLY PHE PHE PRO VAL LEU n/a n/a
28 3QDJ - ALA ALA GLY ILE GLY ILE LEU THR VAL n/a n/a
29 5C09 - TYR LEU GLY GLY PRO ASP PHE PRO THR ILE n/a n/a
30 5C0A - MET VAL TRP GLY PRO ASP PRO LEU TYR VAL n/a n/a
31 5C08 - ARG GLN TRP GLY PRO ASP PRO ALA ALA VAL n/a n/a
32 5C0B - ARG GLN PHE GLY PRO ASP PHE PRO THR ILE n/a n/a
33 5C07 - TYR GLN PHE GLY PRO ASP PHE PRO ILE ALA n/a n/a
34 5C0C - ARG GLN PHE GLY PRO ASP TRP ILE VAL ALA n/a n/a
35 5BS0 Kd = 76.7 nM GLU SER ASP PRO ILE VAL ALA GLN TYR n/a n/a
36 1MI5 Kd ~ 10 uM PHE LEU ARG GLY ARG ALA TYR GLY LEU n/a n/a
37 3VXS - ARG TYR PRO LEU THR LEU GLY TRP CYS PHE n/a n/a
38 3VXR - ARG TYR PRO LEU THR PHE GLY TRP CYS PHE n/a n/a
39 1MWA - GLU GLN TYR LYS PHE TYR SER VAL n/a n/a
40 4G9F - LYS ARG TRP ILE ILE MET GLY LEU ASN LYS n/a n/a
41 4G8G - LYS ARG TRP ILE ILE LEU GLY LEU ASN LYS n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ARG GLY PRO GLY ARG ALA PHE VAL THR ILE; Similar ligands found: 91
No: Ligand ECFP6 Tc MDL keys Tc
1 ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 1 1
2 ILE GLY PRO GLY ARG ALA PHE TYR THR ILE 0.791946 0.890411
3 ILE GLY PRO GLY ARG ALA PHE TYR ALA 0.662338 0.849315
4 ASN TYR THR PRO GLY PRO GLY ILE ARG PHE 0.576471 0.891892
5 ASN TYR THR PRO GLY PRO GLY THR ARG PHE 0.56213 0.878378
6 ARG GLN PHE GLY PRO ASP PHE PRO THR ILE 0.561404 0.943662
7 ARG ABA VAL ILE PHE ALA ASN ILE 0.513158 0.73913
8 LEU PRO PHE GLU ARG ALA THR VAL MET 0.508571 0.916667
9 PHE LEU ARG GLY ARG ALA TYR VAL LEU 0.506173 0.712329
10 PHE LEU TRP GLY PRO ARG ALA LEU VAL 0.505682 0.835616
11 LEU PRO PHE GLU ARG ALA THR ILE MET 0.5 0.930556
12 GLY ARG PRO ARG THR THR SER PHE ALA GLU 0.5 0.942029
13 ARG PRO MET THR PHE LYS GLY ALA LEU 0.488764 0.90411
14 ARG ABA PHE ILE PHE ALA ASN ILE 0.48366 0.704225
15 ARG PRO GLY ASN PHE LEU GLN SER SER PRO 0.483146 0.915493
16 ALA ASN SER ARG PHE PRO THR SER ILE ILE 0.482558 0.942857
17 ARG GLN PHE GLY PRO ASP TRP ILE VAL ALA 0.479167 0.863014
18 ARG TYR GLY PHE VAL ALA ASN PHE 0.47205 0.702703
19 ARG ARG LEU PRO ILE PHE SER ARG LEU 0.464706 0.956522
20 LEU PRO PHE ASP ARG THR THR ILE MET 0.463277 0.944444
21 ARG PRO GLY ASN PHE PHE GLN SER ARG PRO 0.462857 0.837838
22 ARG VAL ALA SER PRO THR SER GLY VAL 0.459627 0.913043
23 ILE PRO ALA TYR GLY VAL LEU THR ILE 0.458824 0.830986
24 PHE GLN PRO GLN ASN GLY GLN PHE ILE 0.45509 0.802817
25 PHE LEU ARG GLY ARG ALA TYR GLY LEU 0.453416 0.712329
26 GLU GLU PHE GLY ARG ALA PHE SER PHE 0.453416 0.704225
27 TYR LEU GLY GLY PRO ASP PHE PRO THR ILE 0.453039 0.835616
28 LEU GLN ARG VAL LEU SEP ALA PRO PHE 0.450292 0.815789
29 VAL MET ALA PRO ARG THR LEU PHE LEU 0.448864 0.890411
30 ARG PHE PRO LEU THR PHE GLY TRP 0.448649 0.90411
31 ARG PRO GLY ASN PHE LEU GLN SER ARG PRO 0.448087 0.902778
32 ARG PRO PRO GLY PHE SER PRO PHE ALA 0.447674 0.847222
33 DPN PRO DAR ILE NH2 0.443709 0.838235
34 DPN PRO DAR DTH NH2 0.443709 0.867647
35 ARG THR TYR SEP GLY PRO MET ASN LYS VAL 0.441026 0.807229
36 ARG VAL ALA SEP PRO THR SER GLY VAL 0.438596 0.84
37 ILE ARG TYR PRO LYS THR PHE GLY TRP 0.438144 0.88
38 ARG PRO GLY ASN PHE LEU GLN SER ARG LEU 0.437158 0.915493
39 GLY ARG PHE ALA ALA ALA ILE ALA LYS 0.435897 0.75
40 ALA ASN SER ARG VAL PRO THR SER ILE ILE 0.435583 0.927536
41 ARG PRO MET THR TYR LYS GLY ALA LEU 0.435484 0.868421
42 ARG TYR PRO LEU THR PHE GLY TRP 0.434555 0.88
43 PHE ARG SER LYS GLY GLU GLU LEU PHE THR 0.432749 0.75
44 ILE ARG ALA ALA PRO PRO PRO LEU PHE 0.430233 0.885714
45 ARG SEP PRO VAL PHE SER 0.430233 0.813333
46 ALA ASN SER ARG TYR PRO THR SER ILE ILE 0.426966 0.90411
47 ASN ARG PRO VAL TYR ILE PRO ARG PRO PRO 0.426901 0.887324
48 ARG PHE PRO LEU THR PHE GLY TRP CYS PHE 0.426396 0.905405
49 ASP ARG VAL TYR ILE HIS PRO PHE 0.426316 0.866667
50 ILE LEU GLY PRO PRO GLY SER VAL TYR 0.426136 0.847222
51 ARG VAL ALA GLN LEU GLU GLN VAL TYR ILE 0.42515 0.71831
52 ARG ILE PRO SER TYR ARG TYR ARG TYR 0.424419 0.878378
53 PHE ASN ARG PRO VAL 0.424051 0.884058
54 ALA ASN SER ARG ALA PRO THR SER ILE ILE 0.423529 0.901408
55 LYS PRO VAL LEU ARG THR ALA 0.423313 0.926471
56 SER SER ILE GLU PHE ALA ARG LEU 0.421687 0.782609
57 ARG GLY PHE ALA LEU M3L SER THR HIS GLY 0.421622 0.797468
58 SER GLU ILE GLU PHE ALA ARG LEU 0.420732 0.768116
59 ARG PRO PRO GLY PHE SER PRO PHE ARG 0.419753 0.8
60 GLU PRO GLY GLY SER ARG 0.419355 0.855072
61 ASP PHE GLU GLU ILE PRO GLY GLU PTR 0.418478 0.734177
62 ASP VAL GLN THR GLY ARG ARG PRO TYR GLU 0.417582 0.929577
63 ALA ILE MET PRO ALA ARG PHE TYR PRO LYS 0.416667 0.818182
64 TYR GLN PHE GLY PRO ASP PHE PRO ILE ALA 0.416216 0.808219
65 LEU PHE GLY TYR PRO VAL TYR VAL 0.415205 0.753425
66 ARG PRO LYS ARG ILE ALA 0.415094 0.867647
67 TYR LEU ALA PRO GLY PRO VAL THR ALA 0.414201 0.833333
68 SER LEU SER ARG THR PRO ALA ASP GLY ARG 0.413793 0.913043
69 LEU LEU PHE GLY LYS PRO VAL TYR VAL 0.411111 0.767123
70 ASP PHE GLU GLU ILE PRO GLY GLU TYS LEU 0.409836 0.694118
71 ARG LEU TYR GLN ASN PRO THR THR TYR ILE 0.408602 0.905405
72 LEU GLY TYR GLY PHE VAL ASN TYR ILE 0.408537 0.621622
73 TYR LEU GLU PRO GLY PRO VAL THR VAL 0.408046 0.84507
74 ALA VAL ALA PHE TYR ILE PRO ASP GLN ALA 0.407407 0.726027
75 ARG TYR PRO LEU THR LEU GLY TRP CYS PHE 0.406863 0.881579
76 PHE GLU ALA ILE PRO ALA GLU TYR LEU 0.40678 0.753425
77 LEU LEU PHE GLY TYR PRO VAL TYR VAL 0.40678 0.753425
78 LEU LEU PHE GLY PHE PRO VAL TYR VAL 0.40678 0.753425
79 TYR LEU GLU PRO GLY PRO VAL THR ALA 0.405714 0.84507
80 PHE ALA PRO GLY ASN TYI PRO ALA LEU 0.405556 0.75
81 THR PRO THR ARG ASP VAL ALA THR SER PRO 0.404908 0.913043
82 CYS VAL ASN GLY SER CYS PHE THR VAL 0.404908 0.647887
83 ARG TYR PRO LEU THR PHE GLY TRP CYS PHE 0.404878 0.868421
84 PHE PRO THR LYS ASP VAL ALA LEU 0.404624 0.867647
85 LEU GLU LYS ALA ARG GLY SER THR TYR 0.404494 0.791667
86 PHE GLU ASP ASN PHE VAL PRO 0.403727 0.777778
87 LEU LEU TYR GLY PHE VAL ASN TYR ILE 0.402367 0.621622
88 ASP PHE GLU GLU ILE PRO GLY GLU TYR LEU 0.402174 0.794521
89 ALA ASN SER ARG TRP PRO THR SER ALY ILE 0.40107 0.88
90 PHE GLU ALA ASN GLY ASN LEU ILE 0.4 0.657143
91 ARG GLY TYR VAL TYR GLN GLY LEU 0.4 0.69863
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: 29
This union binding pocket(no: 1) in the query (biounit: 5ivx.bio1) has 42 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1GEG GLC 0.01772 0.43233 6
2 4B1X LAB 0.008162 0.44814 6.18557
3 4B1V LAB 0.02484 0.41826 6.18557
4 3G58 988 0.03516 0.41027 7
5 1TV5 N8E 0.007894 0.45448 7.2165
6 3RV5 DXC 0.01073 0.4412 7.86517
7 4RW3 PLM 0.0252 0.45117 9
8 1DKF BMS 0.004174 0.42849 9
9 4NOS H4B 0.04602 0.40808 9
10 3IX9 MTX 0.0138 0.42055 10
11 5F7U GLC GLC GLC GLC 0.03937 0.41127 10
12 5V4R MGT 0.009867 0.4565 10.2564
13 4ELG 52J 0.01142 0.40905 13
14 4OAS 2SW 0.006698 0.43979 13.5417
15 3B6C SDN 0.0232 0.42791 13.6752
16 1M2Z BOG 0.005265 0.46218 14
17 5K53 STE 0.00974 0.41803 14.5299
18 2JHP GUN 0.04979 0.40357 14.9485
19 4LWU 20U 0.01327 0.42491 15.2941
20 3OKI OKI 0.005255 0.4304 15.4506
21 5ICK FEZ 0.02153 0.40491 15.7205
22 4UCC ZKW 0.01783 0.45569 16
23 4GBD MCF 0.01863 0.40221 16
24 1LNX URI 0.02275 0.43142 19.7531
25 4W9N TCL 0.0407 0.41433 21.6495
26 4XCP PLM 0.02228 0.42569 24.1176
27 5LX9 OLB 0.009896 0.4313 24.7423
28 2BYC FMN 0.02681 0.41291 25.5474
29 5OCA 9QZ 0.0001191 0.5675 47.4654
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