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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
951.2 n/a O=C(N...
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 208 families.
1 5JHD Kd = 37 nM GLY ILE LEU GLY PHE VAL PHE THR LEU n/a n/a
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 62 families.
1 2F53 - SER LEU LEU MET TRP ILE THR GLN CYS n/a n/a
2 6BJ8 - VAL PRO LEU THR GLU ASP ALA GLU LEU n/a n/a
3 6BJ3 Kd = 17 uM ILE PRO LEU THR GLU GLU ALA GLU LEU n/a n/a
4 5JHD Kd = 37 nM GLY ILE LEU GLY PHE VAL PHE THR LEU n/a n/a
5 5C09 - TYR LEU GLY GLY PRO ASP PHE PRO THR ILE n/a n/a
6 5C0A - MET VAL TRP GLY PRO ASP PRO LEU TYR VAL n/a n/a
7 5C08 - ARG GLN TRP GLY PRO ASP PRO ALA ALA VAL n/a n/a
8 5C0B - ARG GLN PHE GLY PRO ASP PHE PRO THR ILE n/a n/a
50% Homology Family (43)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 42 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 6BJ8 - VAL PRO LEU THR GLU ASP ALA GLU LEU n/a n/a
22 6BJ3 Kd = 17 uM ILE PRO LEU THR GLU GLU ALA GLU LEU n/a n/a
23 5JHD Kd = 37 nM GLY ILE LEU GLY PHE VAL PHE THR LEU n/a n/a
24 4NQD - 2LJ C12 H20 N4 O6 CC/C=N/C1=....
25 4LCW - 1VY C12 H16 N4 O7 CC1=C(N(C2....
26 4L4V Kd = 1.65 uM 1VY C12 H16 N4 O7 CC1=C(N(C2....
27 2JCC - ALA LEU TRP GLY PHE PHE PRO VAL LEU n/a n/a
28 2UWE - ALA LEU TRP GLY PHE PHE PRO VAL LEU n/a n/a
29 1LP9 - ALA LEU TRP GLY PHE PHE PRO VAL LEU n/a n/a
30 3QDJ - ALA ALA GLY ILE GLY ILE LEU THR VAL n/a n/a
31 5C09 - TYR LEU GLY GLY PRO ASP PHE PRO THR ILE n/a n/a
32 5C0A - MET VAL TRP GLY PRO ASP PRO LEU TYR VAL n/a n/a
33 5C08 - ARG GLN TRP GLY PRO ASP PRO ALA ALA VAL n/a n/a
34 5C0B - ARG GLN PHE GLY PRO ASP PHE PRO THR ILE n/a n/a
35 5C07 - TYR GLN PHE GLY PRO ASP PHE PRO ILE ALA n/a n/a
36 5C0C - ARG GLN PHE GLY PRO ASP TRP ILE VAL ALA n/a n/a
37 5BS0 Kd = 76.7 nM GLU SER ASP PRO ILE VAL ALA GLN TYR 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
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GLY ILE LEU GLY PHE VAL PHE THR LEU; Similar ligands found: 58
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 0.768519 0.938776
3 GLY ILE TRP GLY PHE VAL PHE THR LEU 0.615385 0.857143
4 GLY ILE LEU GLU PHE VAL PHE THR LEU 0.6 0.94
5 SER LEU PHE ASN THR ILE ALA VAL LEU 0.546154 0.862745
6 ASP ASP ASP MET GLY PHE GLY LEU PHE ASP 0.530973 0.877551
7 ASP ASP MET GLY PHE GLY LEU PHE ASP 0.530973 0.877551
8 LEU VAL THR LEU VAL PHE VAL 0.526316 0.8125
9 PHE LEU THR GLY ILE GLY ILE ILE THR VAL 0.504065 0.9
10 LEU LEU TYR GLY PHE VAL ASN TYR ILE 0.503759 0.886792
11 LEU LEU TYR GLY PHE VAL ASN TYR VAL 0.496183 0.867925
12 LEU GLY TYR GLY PHE VAL ASN TYR ILE 0.481203 0.886792
13 ALA PHE THR SER 0.476636 0.795918
14 VAL GLY ILE THR ASN VAL ASP LEU 0.475806 0.807692
15 ALA LEU GLY ILE GLY ILE LEU THR VAL 0.465517 0.877551
16 LYS VAL ILE THR PHE ILE ASP LEU 0.458647 0.849057
17 ARG ILE PHE SER 0.45082 0.701754
18 LEU SER PRO ASP SER PHE LEU ASN ASP 0.448598 0.816327
19 PHE LEU SER THR LYS 0.447154 0.811321
20 ALA VAL GLY ILE GLY ALA VAL PHE LEU 0.447154 0.795918
21 ALA VAL GLY ILE GLY ALA VAL PHE 0.447154 0.795918
22 CYS VAL ASN GLY SER CYS PHE THR VAL 0.444444 0.830189
23 ALA GLU THR PHE TYR VAL ASP GLY 0.440678 0.784314
24 SER LEU PHE ASN THR VAL ALA THR LEU TYR 0.439716 0.814815
25 LYS ILE LEU GLY PRV VAL PHE PRQ VAL 0.43949 0.642857
26 THR LEU MET THR GLY GLN LEU GLY LEU PHE 0.438017 0.8
27 PHE LEU ARG GLY ARG ALA TYR VAL LEU 0.435374 0.721311
28 GLN VAL ASN PHE LEU GLY LYS 0.433824 0.777778
29 MSE ILE LEU GLY PRV VAL PHE PRQ VAL 0.433121 0.616438
30 ARG GLY PHE ALA LEU M3L SER THR HIS GLY 0.428571 0.605263
31 TYR SER THR CYS TYR PHE ILE MET 0.426471 0.758621
32 GLU THR PHE TYR VAL ASP GLY 0.424242 0.851852
33 ASP SER GLY PHE SER PHE GLY SER LYS 0.422018 0.836735
34 GLY ALA GLU THR PHE TYR VAL ASP GLY ALA 0.421429 0.836364
35 LEU ALA GLY ILE GLY ILE LEU THR VAL 0.419355 0.84
36 GLY ALA ASP ILE PHE TYR LEU ASP GLY ALA 0.41791 0.846154
37 GLY ARG PHE GLN VAL THR 0.416667 0.75
38 ALA ALA GLY ILE GLY ILE LEU THR VAL 0.414634 0.84
39 SER ILE ILE GLY PHE GLU LYS LEU 0.414286 0.849057
40 ARG GLN VAL ASN PHE LEU GLY LYS ILE ASN 0.414062 0.836735
41 SER LEU PHE ASN THR VAL ALA THR LEU 0.411765 0.807692
42 GLU THR VAL ARG PHE GLN SER ASP 0.409722 0.741379
43 THR TYR PHE ALA VAL LEU MET VAL SER 0.409722 0.77193
44 LEU TYR LEU VAL CYS GLY GLU ARG GLY PHE 0.409091 0.737705
45 ALA LEU ALA GLY ILE GLY ILE LEU THR VAL 0.408 0.84
46 FME TYR PHE ILE ASN ILE LEU THR LEU 0.406897 0.762712
47 GLU ASP GLU ASP PHE GLU ILE LEU SER LEU 0.405594 0.796296
48 GLU LEU ALA GLY ILE GLY ILE LEU THR VAL 0.40458 0.823529
49 LYS VAL LEU PHE LEU ASP GLY 0.40458 0.788462
50 SER ARG ILE ARG ILE ARG GLY TYR VAL ARG 0.404255 0.730159
51 GLN PHE LYS ASP ASN VAL ILE LEU LEU 0.40411 0.763636
52 ASP PHE M3L THR ASP 0.403101 0.68254
53 ARG GLN ALA ASN PHE LEU GLY LYS 0.403101 0.823529
54 GLY ASP GLU VAL LYS VAL PHE ARG 0.402778 0.677966
55 TYR GLN GLU SER THR ASP PHE THR PHE LEU 0.401639 0.84
56 LEU LEU PHE GLY TYR PRO VAL TYR VAL 0.401316 0.676923
57 LEU LEU PHE GLY PHE PRO VAL TYR VAL 0.401316 0.676923
58 TYR GLY GLY PHE LEU 0.4 0.830189
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 with APoc: 205
This union binding pocket(no: 1) in the query (biounit: 5jhd.bio1) has 39 residues
No: Leader PDB Ligand Sequence Similarity
1 4DE2 DN3 2.89256
2 1DTL BEP 3.72671
3 5Y79 3PG 4
4 3STD MQ0 4.24242
5 3RV5 DXC 4.49438
6 5Z3I ADE 4.69484
7 4JZB P2H 5
8 4JZX 476 5
9 4K10 NI9 5
10 6BR8 PGV 5.16432
11 3B6C SDN 5.55556
12 3ETG GTP 5.6338
13 4V1F BQ1 5.81395
14 2BYC FMN 5.83942
15 6BR9 PGV 6
16 4B1V LAB 6
17 5TZO 7V7 6
18 5NM7 GLY 6
19 1R6N 434 6.16114
20 1NU4 MLA 6.18557
21 4YLZ LAT NAG GAL 6.53595
22 3E70 GDP 6.70732
23 4DOO DAO 6.82927
24 4UCC ZKW 7
25 1UUY PPI 7
26 3X01 AMP 7
27 2QES ADE 7.02479
28 2GWH PCI 7.04225
29 1M2Z BOG 7.04225
30 5V3Y 5V8 7.04225
31 5WKC F50 7.04225
32 3UST FAD 7.11611
33 1XNK XS2 7.14286
34 3O01 DXC 7.51174
35 1YC4 43P 7.51174
36 3SQP 3J8 7.85124
37 4J24 EST 7.91667
38 4J26 EST 7.91667
39 6B21 C9V 7.98122
40 2IGA XX3 7.98122
41 2WOR 2AN 8
42 6CB2 OLC 8
43 3FAL REA 8
44 3W54 RNB 8
45 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 8
46 3ROE THM 8
47 5XQL C2E 8.26446
48 2RH1 CLR 8.4507
49 5OLK DTP 8.67769
50 1NF8 BOG 8.69565
51 5FPN KYD 8.69565
52 3GWN FAD 8.77193
53 4F06 PHB 8.92019
54 1A78 TDG 8.95522
55 2BHW NEX 9
56 6FBA D48 9
57 2WDA L42 9
58 6BMS PLM 9
59 4WX0 HXD 9
60 4B7H NDP 9
61 2Z3U CRR 9
62 2I56 RNS 9.05797
63 1WMA AB3 9.09091
64 4EE7 PIS 9.09091
65 5V4R MGT 9.25926
66 4WGF HX2 9.26829
67 2D24 XYS XYS 9.42029
68 4RC8 STE 9.45946
69 4G86 BNT 9.50413
70 1XVB 3BR 9.50413
71 3KO0 TFP 9.90099
72 2D5X L35 9.92908
73 6DIO CIT 10
74 4XCP PLM 10
75 3GXO MQA 10
76 5M36 9SZ 10
77 5K52 OCD 10
78 4URN NOV 10
79 5M37 9SZ 10
80 5H5A 6OU 10
81 4P7X AKG 10
82 4P7X YCP 10
83 2CB8 MYA 10.3448
84 1TW4 CHD 10.4
85 4HK8 XYP XYP XYP XYP XYP XYP 10.582
86 3CBC DBS 10.6061
87 1AUA BOG 10.7438
88 5IUY BOG 10.8696
89 3AQT RCO 10.8696
90 5OSW DIU 10.8696
91 1SLT NDG GAL 11
92 2B99 RDL 11
93 4MGA 27L 11
94 3CHT 4NB 11
95 4TV1 36M 11
96 1XMY ROL 11
97 5K53 STE 11
98 5UGW GSH 11
99 5DX3 EST 11
100 4MG7 27H 11
101 4HBM 0Y7 11
102 2C3Q GTX 11
103 2BJ4 OHT 11
104 5DXG EST 11
105 3UUD EST 11
106 4TUZ 36J 11
107 5HYR EST 11
108 5Y02 HBX 11.215
109 5Y02 MXN 11.215
110 4OKD GLC GLC GLC 11.2676
111 2IYG FMN 11.2903
112 2QL9 CIT 11.3402
113 5WSY 7UC 11.5607
114 3HLX PQQ 11.6279
115 3WUD GLC GAL 11.7647
116 2VWA PTY 11.8812
117 6BVM EBV 12
118 6BVK EAV 12
119 6BVJ EAS 12
120 6BVL EBY 12
121 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 12
122 6BVI EC4 12
123 3GFZ FMN 12
124 6D56 FVM 12
125 4W9N TCL 12
126 3N0Y APC 12
127 6D5G FVD 12
128 5WRE 7TL 12
129 5N26 CPT 12.0879
130 2BCG GER 12.1359
131 1H4H XYP XYS XYP 12.4402
132 3KP6 SAL 12.5828
133 5X13 HC4 13
134 4YSX E23 13
135 5JOG 6LT 13
136 5AWV GHP 3MY 3FG GHP GHP OMY 3FG NAG MAN 13
137 4A38 BZS 13
138 6CGN DA 13.1455
139 3QRC SCR 13.3758
140 3HP9 CF1 13.6364
141 5CHR 4NC 13.8686
142 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 14
143 3AHQ FAD 14
144 6FWH 5LD 14
145 5N8V KZZ 14.4928
146 1T0S BML 15
147 1J78 VDY 15
148 2CIX CEJ 15
149 4IBF 1D5 15
150 2QJY UQ2 15
151 4YUS FMN 15
152 1ELR ACE MET GLU GLU VAL ASP 15.2672
153 4F4S EFO 15.7895
154 3F8C HT1 15.873
155 1TV5 N8E 16
156 1J3R 6PG 16
157 3R9V DXC 17
158 1MAI I3P 17
159 4OWK NGA 17
160 1RV1 IMZ 17.6471
161 1HBK MYR 17.9775
162 4DK7 0KS 18
163 5IM3 DTP 18
164 4LO2 GAL BGC 18
165 3KFC 61X 18
166 3ANK NG6 GCD 18
167 2V5E SCR 18.8119
168 6BJO DUY 19
169 3L0E G58 19
170 5X3R 7Y3 19
171 2Y69 CHD 19.0476
172 5N7O 69Y 19.457
173 2HFN FMN 19.6078
174 2XOM GAL GAL GAL 19.7368
175 5MWE TCE 20
176 2ZQO NGA 20
177 2HHP FLC 21.1268
178 5U9J GER 21.8935
179 2QCX PF1 22
180 1LFO OLA 22
181 2HZL PYR 22
182 5UC9 MYR 22
183 5XJ7 87O 22.8856
184 4OGQ 7PH 23.5294
185 4OGQ 1O2 23.5294
186 4OGQ SQD 23.5294
187 5V03 658 23.5294
188 1X0P FAD 25
189 5ZCO PEK 25.5319
190 5W97 CHD 25.5319
191 5Z84 PEK 25.5319
192 5Z84 CHD 25.5319
193 5ZCO CHD 25.5319
194 2DYR PGV 25.5319
195 5LX9 OLB 25.8216
196 4P7U 1PS 25.8929
197 5W7B MYR 26
198 3HNC TTP 26
199 5AZC PGT 29
200 6GMN F4E 31.9588
201 5VRH OLB 32
202 2UW1 GVM 32
203 5NNT DPV 37.8378
204 5C1M OLC 42.4
205 5OCA 9QZ 49.7696
Pocket No.: 2; Query (leader) PDB : 5JHD; Ligand: GLY ILE LEU GLY PHE VAL PHE THR LEU; Similar sites found with APoc: 19
This union binding pocket(no: 2) in the query (biounit: 5jhd.bio1) has 39 residues
No: Leader PDB Ligand Sequence Similarity
1 3P9T TCL 5.02283
2 1W3T 3GR 5.07246
3 2YMZ LAT 5.38462
4 3KYQ DPV 6.53266
5 4UMJ BFQ 7.43802
6 3FAL LO2 8
7 4D06 X8W 10
8 5JSD ACY 1GN GAL 1GN BGC ACY GAL BGC 10
9 4XO8 KGM 10.7595
10 5OVV ACE ILE GLU SER THR GLU ILE 12
11 4C01 QY9 12.3188
12 2PA7 TYD 12.766
13 1J1R ADE 13
14 3ZW2 NAG GAL FUC 14.9425
15 4D4U FUC 16.4319
16 2P7Q GG6 17
17 1ZED PNP 18
18 1ZGA HMK 23
19 2HRL SIA GAL SIA BGC NGA CEQ 32.2835
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