Receptor
PDB id Resolution Class Description Source Keywords
5JHD 2.46 Å NON-ENZYME: IMMUNE CRYSTAL STRUCTURE OF LS10-TCR/M1-HLA-A*02 COMPLEX HOMO SAPIENS TCR-HLA*A2 M1 INFLUENZA MATRIX PROTEIN IMMUNE SYSTEM
Ref.: BROAD TCR REPERTOIRE AND DIVERSE STRUCTURAL SOLUTIO RECOGNITION OF AN IMMUNODOMINANT CD8(+) T CELL EPIT NAT. STRUCT. MOL. BIOL. V. 24 395 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDT J:301;
E:301;
Invalid;
Invalid;
none;
none;
submit data
292.243 C10 H16 N2 O8 C(CN(...
GLY ILE LEU GLY PHE VAL PHE THR LEU H:1;
C:1;
Valid;
Valid;
none;
none;
Kd = 37 nM
966.191 n/a O=C([...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5JHD 2.46 Å NON-ENZYME: IMMUNE CRYSTAL STRUCTURE OF LS10-TCR/M1-HLA-A*02 COMPLEX HOMO SAPIENS TCR-HLA*A2 M1 INFLUENZA MATRIX PROTEIN IMMUNE SYSTEM
Ref.: BROAD TCR REPERTOIRE AND DIVERSE STRUCTURAL SOLUTIO RECOGNITION OF AN IMMUNODOMINANT CD8(+) T CELL EPIT NAT. STRUCT. MOL. BIOL. V. 24 395 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 5JHD Kd = 37 nM GLY ILE LEU GLY PHE VAL PHE THR LEU 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: GLY ILE LEU GLY PHE VAL PHE THR LEU; Similar ligands found: 82
No: Ligand ECFP6 Tc MDL keys Tc
1 GLY ILE LEU GLY PHE VAL PHE THR LEU 1 1
2 GLY ILE LEU GLY LEU VAL PHE THR LEU 0.947917 0.958333
3 GLY ILE TRP GLY PHE VAL PHE THR LEU 0.745763 0.872727
4 GLY ILE LEU GLU PHE VAL PHE THR LEU 0.740741 0.938776
5 PHE LEU THR GLY ILE GLY ILE ILE THR VAL 0.555556 0.918367
6 LYS VAL ILE THR PHE ILE ASP LEU 0.553719 0.846154
7 LEU LEU TYR GLY PHE VAL ASN TYR ILE 0.542636 0.886792
8 SER LEU PHE ASN THR ILE ALA VAL LEU 0.540323 0.846154
9 LEU GLY TYR GLY PHE VAL ASN TYR ILE 0.531746 0.886792
10 ALA LEU GLY ILE GLY ILE LEU THR VAL 0.518182 0.895833
11 LEU LEU TYR GLY PHE VAL ASN TYR VAL 0.515625 0.867925
12 THR LEU MET THR GLY GLN LEU GLY LEU PHE 0.504425 0.8
13 PHE LEU ARG GLY ARG ALA TYR VAL LEU 0.50365 0.721311
14 SER ILE ILE GLY PHE GLU LYS LEU 0.5 0.865385
15 SER LEU PHE ASN THR VAL ALA THR LEU 0.5 0.807692
16 TYR GLN GLU SER THR ASP PHE THR PHE LEU 0.5 0.857143
17 GLN VAL ASN PHE LEU GLY LYS 0.5 0.777778
18 TYR GLY GLY PHE LEU 0.5 0.846154
19 CYS VAL ASN GLY SER CYS PHE THR VAL 0.492188 0.830189
20 LEU VAL THR LEU VAL PHE VAL 0.486957 0.791667
21 ASP ASP MET GLY PHE GLY LEU PHE ASP 0.482456 0.895833
22 ASP ASP ASP MET GLY PHE GLY LEU PHE ASP 0.482456 0.895833
23 FME TYR PHE ILE ASN ILE LEU THR LEU 0.481481 0.762712
24 GLY ALA GLU THR PHE TYR VAL ASP GLY ALA 0.477273 0.851852
25 ILE LEU ALA LYS PHE LEU HIS THR LEU 0.471014 0.733333
26 GLN PHE LYS ASP ASN VAL ILE LEU LEU 0.466667 0.745455
27 SER ARG ILE ARG ILE ARG GLY TYR VAL ARG 0.466165 0.730159
28 ARG GLY TYR VAL TYR GLN GLY LEU 0.462121 0.733333
29 LEU ASP GLU GLU THR GLY GLU PHE LEU 0.457364 0.882353
30 GLU THR PHE TYR VAL ASP GLY 0.456693 0.867925
31 ALA LEU ALA GLY ILE GLY ILE LEU THR VAL 0.453782 0.857143
32 ALA ALA GLY ILE GLY ILE LEU THR VAL 0.449153 0.857143
33 GRN NVA ALA GLY ILE GLY ILE LEU THR LPH 0.447761 0.849057
34 ILE ARG LYS ILE LEU PHE LEU ASP GLY ILE 0.447552 0.7
35 LYS VAL LEU PHE LEU ASP GLY 0.447154 0.803922
36 ILE LEU SER ALA LEU VAL GLY ILE LEU 0.446281 0.836735
37 LEU TYR LEU VAL CYS GLY GLU ARG GLY PHE 0.445205 0.737705
38 SER SER VAL ILE GLY VAL TRP TYR LEU 0.441379 0.79661
39 ILE LEU GLY LYS PHE LEU HIS ARG LEU 0.440559 0.636364
40 LEU ALA GLY ILE GLY ILE LEU THR VAL 0.438017 0.857143
41 GLY ALA GLU VAL PHE TYR VAL ASP GLY ALA 0.431818 0.830189
42 ILE ILE SER ALA VAL VAL GLY ILE LEU 0.429752 0.836735
43 GLU ASP GLU ASP PHE GLU ILE LEU SER LEU 0.42963 0.811321
44 ARG GLN ALA ASN PHE LEU GLY LYS 0.427419 0.823529
45 LYS LYS SER LYS THR LYS CYS VAL ILE PHE 0.42623 0.86
46 SER LEU TYR LEU THR VAL ALA THR LEU 0.424 0.773585
47 ALA LEU TRP GLY PHE VAL PRO VAL LEU 0.422078 0.646154
48 GLU LEU ALA ALA ILE GLY ILE LEU THR VAL 0.421875 0.857143
49 ARG TYR GLY PHE VAL ALA ASN PHE 0.421429 0.737705
50 ALA ILE PHE GLN SER SER MET THR LYS 0.42029 0.745763
51 PHE GLU ALA ASN GLY ASN LEU ILE 0.419118 0.811321
52 ARG PRO MET THR PHE LYS GLY ALA LEU 0.41875 0.608108
53 GLU ALA ALA GLY ILE GLY ILE LEU THR VAL 0.418605 0.84
54 SER ILE ILE ASN PHE GLU LYS LEU 0.41791 0.8
55 GLY ALA GLN THR PHE TYR VAL ASP GLY ALA 0.41791 0.851852
56 GLU LEU ALA GLY ILE GLY ILE LEU THR VAL 0.417323 0.84
57 SER LEU TYR ASN THR ILE ALA THR LEU 0.416667 0.8
58 SER LEU TYR ASN VAL VAL ALA THR LEU 0.416667 0.763636
59 LEU LEU PHE GLY TYR PRO VAL TYR VAL 0.416107 0.6875
60 LEU LEU PHE GLY PHE PRO VAL TYR VAL 0.416107 0.6875
61 ILE ASN PHE ASP PHE ASN THR ILE 0.414634 0.826923
62 GLY ASN TYR SER PHE TYR ALA LEU 0.414062 0.836364
63 THR PHE LYS LYS THR ASN 0.413223 0.745455
64 LEU LEU PHE GLY LYS PRO VAL TYR VAL 0.411765 0.703125
65 CYS THR PHE LYS THR LYS THR ASN 0.41129 0.75
66 PHE LEU ARG GLY ARG ALA TYR GLY LEU 0.410072 0.721311
67 ILE PRO ALA TYR GLY VAL LEU THR ILE 0.409396 0.71875
68 SER LEU TYR ASN THR VAL ALA THR LEU 0.409091 0.763636
69 GLU ILE ILE ASN PHE GLU LYS LEU 0.407407 0.759259
70 LEU PHE GLY TYR PRO VAL TYR VAL 0.406897 0.6875
71 ALA LEU TRP GLY PHE PHE PRO VAL LEU 0.406452 0.646154
72 GLY GLY LYS LYS LYS TYR LYS LEU 0.404959 0.763636
73 SER SER ILE GLU PHE ALA ARG LEU 0.404255 0.745763
74 THR LYS CYS VAL PHE MET 0.403101 0.767857
75 SER GLU ILE GLU PHE ALA ARG LEU 0.402878 0.758621
76 SER SER VAL VAL GLY VAL TRP TYR LEU 0.402778 0.779661
77 MSE ILE LEU GLY PRV VAL PHE PRQ VAL 0.402439 0.611111
78 GLY GLY LYS LYS LYS TYR GLN LEU 0.401575 0.75
79 SER LEU PHE ASN THR VAL ALA THR LEU TYR 0.401408 0.781818
80 PRO GLU GLY ASP PM3 GLU GLU VAL LEU 0.4 0.706897
81 ALA GLU THR PHE TYR VAL ASP GLY 0.4 0.792453
82 SER LEU ASN TYR ILE ILE LYS VAL LYS GLU 0.4 0.762712
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5JHD; Ligand: GLY ILE LEU GLY PHE VAL PHE THR LEU; Similar sites found: 45
This union binding pocket(no: 1) in the query (biounit: 5jhd.bio1) has 39 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3RV5 DXC 0.01573 0.45159 4.49438
2 4JZB P2H 0.002798 0.46008 5
3 4JZX 476 0.009568 0.42545 5
4 3B6C SDN 0.01368 0.43773 5.55556
5 2BYC FMN 0.04111 0.40065 5.83942
6 4B1V LAB 0.0283 0.41256 6
7 4DOO DAO 0.02707 0.40035 6.82927
8 4UCC ZKW 0.005232 0.47271 7
9 2QES ADE 0.0297 0.42377 7.02479
10 1YC4 43P 0.04148 0.40044 7.51174
11 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 0.0388 0.40534 8
12 1A78 TDG 0.004626 0.46085 8.95522
13 2WDA L42 0.04552 0.4127 9
14 4B7H NDP 0.02504 0.40198 9
15 4EE7 PIS 0.03701 0.40679 9.09091
16 5V4R MGT 0.009997 0.44647 9.25926
17 2D24 XYS XYS 0.002076 0.48779 9.42029
18 4XCP PLM 0.01689 0.43119 10
19 4URN NOV 0.04586 0.40881 10
20 4HK8 XYP XYP XYP XYP XYP XYP 0.01445 0.40166 10.582
21 4MGA 27L 0.02245 0.43131 11
22 3CHT 4NB 0.03046 0.42074 11
23 5K53 STE 0.0083 0.4183 11
24 4MG7 27H 0.02074 0.40591 11
25 4HBM 0Y7 0.03789 0.40589 11
26 2BJ4 OHT 0.01571 0.40559 11
27 3UUD EST 0.03453 0.40128 11
28 4W9N TCL 0.039 0.41272 12
29 2BCG GER 0.04112 0.4076 12.1359
30 1H4H XYP XYS XYP 0.008629 0.42763 12.4402
31 5AWV GHP 3MY 3FG GHP GHP OMY 3FG NAG MAN 0.03879 0.41218 13
32 3HP9 CF1 0.002417 0.4878 13.6364
33 3AHQ FAD 0.007191 0.41503 14
34 2QJY UQ2 0.04258 0.4106 15
35 1TV5 N8E 0.03123 0.42482 16
36 3R9V DXC 0.03618 0.41737 17
37 1MAI I3P 0.03087 0.41734 17
38 4DK7 0KS 0.003368 0.43978 18
39 3L0E G58 0.003894 0.4151 19
40 5U9J GER 0.04929 0.40706 21.8935
41 1LFO OLA 0.007841 0.42268 22
42 5UC9 MYR 0.02633 0.4072 22
43 5LX9 OLB 0.01832 0.41508 25.8216
44 5VRH OLB 0.01042 0.44771 32
45 5OCA 9QZ 0.0002445 0.55023 49.7696
Pocket No.: 2; Query (leader) PDB : 5JHD; Ligand: GLY ILE LEU GLY PHE VAL PHE THR LEU; Similar sites found: 5
This union binding pocket(no: 2) in the query (biounit: 5jhd.bio1) has 39 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3P9T TCL 0.04108 0.40403 5.02283
2 2YMZ LAT 0.04338 0.40021 5.38462
3 3KYQ DPV 0.006036 0.45713 6.53266
4 4C01 QY9 0.03035 0.40999 12.3188
5 1J1R ADE 0.02036 0.431 13
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