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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 208 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 62 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 (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: ARG GLY PRO GLY ARG ALA PHE VAL THR ILE; Similar ligands found: 74
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 0.467033 0.915493
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 LEU GLN ARG VAL LEU SEP ALA PRO PHE 0.453488 0.802632
26 ARG ABA VAL ILE PHE ALA ASN ILE 0.453416 0.724638
27 ARG TYR GLY PHE VAL ALA ASN PHE 0.451807 0.689189
28 SER SER TYR ARG ARG PRO VAL GLY ILE 0.451429 0.943662
29 ARG ILE PRO SER TYR ARG TYR ARG TYR 0.449102 0.890411
30 ARG ARG LEU PRO ILE PHE SER ARG LEU 0.448276 0.942029
31 GLY ARG PHE GLN VAL THR 0.448052 0.746269
32 ARG PHE PRO LEU THR PHE GLY TRP 0.446809 0.890411
33 GLU GLU PHE GLY ARG ALA PHE SER PHE 0.442424 0.690141
34 DPN PRO DAR DTH NH2 0.441558 0.895522
35 VAL MET ALA PRO ARG THR LEU PHE LEU 0.438889 0.876712
36 ALA VAL ALA PHE TYR ILE PRO ASP GLN ALA 0.4375 0.75
37 ARG VAL ALA SER PRO THR SER GLY VAL 0.436364 0.898551
38 ASP PHE GLU GLU ILE PRO GLY GLU PTR 0.431694 0.734177
39 ARG TYR PRO LEU THR PHE GLY TRP CYS PHE 0.431373 0.88
40 ALA ASN SER ARG PHE PRO THR SER ILE ILE 0.430939 0.928571
41 ARG TYR PRO LEU THR PHE GLY TRP 0.430769 0.866667
42 ARG PRO PRO GLY PHE 0.43038 0.823529
43 ASN PHE ASP ASN PRO VAL TYR ARG LYS THR 0.429319 0.878378
44 ARG THR TYR SEP GLY PRO MET ASN LYS VAL 0.427136 0.795181
45 ARG ABA PHE ILE PHE ALA ASN ILE 0.425926 0.690141
46 ASN ARG PRO VAL TYR ILE PRO ARG PRO PRO 0.425287 0.9
47 THR PRO ARG VAL THR GLY GLY GLY ALA MET 0.425287 0.876712
48 ARG PHE PRO LEU THR PHE GLY TRP CYS PHE 0.425 0.891892
49 ILE ARG TYR PRO LYS THR PHE GLY TRP 0.423645 0.866667
50 DPN PRO DAR ILE NH2 0.423077 0.850746
51 GLU THR VAL ARG PHE GLN SER ASP 0.422619 0.73913
52 ILE ARG ALA ALA PRO PRO PRO LEU PHE 0.420455 0.871429
53 ARG PRO PRO ILE PHE ILE ARG ARG LEU 0.420455 0.884058
54 ARG ILE PHE SER 0.42 0.705882
55 ASP PHE GLU GLU ILE PRO GLY GLU TYR LEU 0.418478 0.794521
56 ARG VAL ALA SEP PRO THR SER GLY VAL 0.417143 0.826667
57 LEU PRO PHE ASP ARG THR THR ILE MET 0.416216 0.930556
58 SER LEU SER ARG THR PRO ALA ASP GLY ARG 0.414773 0.898551
59 MET CYS PRO ARG MET THR ALA VAL MET 0.412429 0.875
60 PHE LEU ARG GLY ARG ALA TYR GLY LEU 0.410714 0.69863
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 ASP VAL GLN THR GLY ARG ARG PRO TYR GLU 0.406417 0.915493
65 ALA ILE MET PRO ALA ARG PHE TYR PRO LYS 0.406091 0.805195
66 ARG TYR PRO LEU THR LEU GLY TRP CYS PHE 0.405797 0.868421
67 LEU LEU PHE GLY LYS PRO VAL TYR VAL 0.405556 0.756757
68 ALA ILE ALA TYR PHE ILE PRO ASP GLN ALA 0.404908 0.736111
69 ARG ARG ALA SEP ALA PRO LEU PRO 0.404624 0.789474
70 DPN PRO DAR CYS NH2 0.403846 0.794118
71 ILE SER PRO ARG THR LEU ASP ALA TRP 0.40201 0.917808
72 ALA THR ARG ASN PHE SER GLY 0.401235 0.753623
73 ILE LEU GLY PRO PRO GLY SER VAL TYR 0.4 0.847222
74 GLY ARG PHE ALA ALA ALA ILE ALA LYS 0.4 0.735294
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: 213
This union binding pocket(no: 1) in the query (biounit: 5ivx.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
1 3KPE TM3 None
2 4WG0 CHD None
3 3K0T BGC 2.0979
4 1XMY ROL 3.4188
5 5M36 9SZ 3.93013
6 4F4S EFO 3.94737
7 5BSH PRO 4
8 3T03 3T0 4
9 2HFP NSI 4
10 1NU4 MLA 4.12371
11 6BR8 6OU 4.12371
12 6BR8 PGV 4.12371
13 6C1R EFD 4.33213
14 6DIO CIT 4.70085
15 1TMX HGX 4.70085
16 5IUY BOG 5.05415
17 4K10 NI9 5.15464
18 4JZB P2H 5.15464
19 4M52 M52 5.15464
20 5OF9 ANP 5.41516
21 4B7H NDP 5.6701
22 1YKD CMP 5.6701
23 5CHR 4NC 5.83942
24 5MBC FMN 5.98291
25 3TDC 0EU 6
26 5AZC PGT 6
27 1GEG GLC 6
28 1JGS SAL 6
29 4B2D SER 6
30 1B74 DGN 6
31 5YEE LAB 6.18557
32 4B1X LAB 6.18557
33 5ZZA LAB 6.18557
34 5ZZB LAB 6.18557
35 4B1V LAB 6.18557
36 4DOO DAO 6.34146
37 1XVB 3BR 6.41026
38 5Y4K AKR 6.41026
39 3ROE THM 6.41509
40 2PRG BRL 6.81818
41 2RH1 CLR 6.85921
42 1NF8 BOG 7
43 4WGF HX2 7
44 2WPW ACO 7
45 6BMS POV 7
46 2BJ4 OHT 7
47 3G58 988 7
48 2WPX ACO 7
49 2PX6 DH9 7
50 1BGQ RDC 7
51 5V3Y 5V8 7.2165
52 1TV5 N8E 7.2165
53 3LDW ZOL 7.22022
54 5N8V KZZ 7.24638
55 2IYG FMN 7.25806
56 5UC4 83S 7.27273
57 2CIX CEJ 7.35786
58 5TVI O8N 7.6087
59 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 7.69231
60 5YB7 ORN 7.69231
61 5NM7 GLY 7.69231
62 3RV5 DXC 7.86517
63 2YLD CMO 7.87402
64 5KAU RHQ 7.87879
65 1SNN 5RP 7.92952
66 1E4I NFG 8
67 4TV1 36M 8
68 4MGA 27L 8
69 2QCX PF1 8
70 5HYR EST 8
71 5WGQ EST 8
72 5WGD EST 8
73 4TUZ 36J 8
74 2QZO KN1 8
75 3KMZ EQO 8
76 4MG7 27H 8
77 1W96 S1A 8
78 2HJ3 FAD 8
79 4MGD 27N 8
80 1J78 VDY 8.11966
81 5KZD RCJ 8.24742
82 1XQP 8HG 8.24742
83 3ANP DAO 8.33333
84 3ANP DCC 8.33333
85 5XJ7 87O 8.45771
86 1AUA BOG 8.54701
87 2HHP FLC 8.76289
88 2VWA PTY 8.91089
89 6D5V FVY 8.98204
90 6D5M FW4 8.98204
91 6CB2 OLC 9
92 4RW3 PLM 9
93 6B21 C9V 9
94 6D5L FW7 9
95 1DKF BMS 9
96 6D5J FV4 9
97 6BVM EBV 9
98 2CUN 3PG 9
99 4RYV ZEA 9
100 4NB5 2JT 9
101 4G86 BNT 9
102 4NOS H4B 9
103 3FAL REA 9
104 2HZL PYR 9
105 2O1V ADP 9.27835
106 6EVN PRO PRO GLY PRO ALA GLY PRO PRO GLY 9.80392
107 5B4B LP5 9.82906
108 3IX9 MTX 10
109 3NB0 G6P 10
110 4DXJ 0M9 10
111 5F7U GLC GLC GLC GLC 10
112 1RY2 AMP 10
113 5JOG 6LT 10
114 4RLT FSE 10.2041
115 5X3R 7Y3 10.2439
116 5V4R MGT 10.2564
117 1DGH NDP 10.3093
118 1R6N 434 10.4265
119 3E70 GDP 10.6838
120 4QO5 NAG 10.8247
121 6BR9 PGV 10.8303
122 6BR9 6OU 10.8303
123 4HBM 0Y7 10.8333
124 2P1C GG3 11
125 2BCG GER 11.3402
126 4D52 GIV 11.3402
127 6F5W KG1 11.3402
128 2OZ5 7XY 11.5385
129 5IM3 DTP 11.5523
130 1UBY DMA 11.8557
131 3F8C HT1 11.9048
132 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 12
133 2WOR 2AN 12
134 5XQL C2E 12
135 2F69 SAH 12
136 4I67 G G G RPC 12.6437
137 1TIQ COA 12.7778
138 2GWH PCI 13
139 2WDQ CBE 13
140 4IBF 1D5 13
141 4ELG 52J 13
142 5W99 A1V 13
143 4OAS 2SW 13.5417
144 3B6C SDN 13.6752
145 2ZPA ACO 13.7184
146 2HFN FMN 13.7255
147 3GFZ FMN 13.9175
148 1M2Z BOG 14
149 3R9C ECL 14
150 5CX6 CDP 14
151 1DTL BEP 14
152 3QKD HI0 14
153 4OKD GLC GLC GLC 14.1026
154 5K53 STE 14.5299
155 1XNK XS2 14.7959
156 2JHP GUN 14.9485
157 5UNJ RJW 15
158 3BEJ MUF 15.126
159 4LWU 20U 15.2941
160 3OKI OKI 15.4506
161 2BHW XAT 15.4639
162 3RMK BML 15.4639
163 2BHW NEX 15.4639
164 5ICK FEZ 15.7205
165 3KO0 TFP 15.8416
166 4UCC ZKW 16
167 3W54 RNB 16
168 5VRH OLB 16
169 3AQT RCO 16
170 4GBD MCF 16
171 3I6B KDO 16.6667
172 3GWN FAD 16.6667
173 4DK7 0KS 17
174 5TZO 7V7 17
175 5V03 658 17
176 5W7B MYR 18.0412
177 5OLK DTP 18.0412
178 3SP6 IL2 19
179 1RVV INI 19
180 1D8C SOR 19.0722
181 4YSX E23 19.2308
182 1LNX URI 19.7531
183 4V1F BQ1 20.9302
184 4UA3 COA 21
185 5OM2 DXT 21.3675
186 4W9N TCL 21.6495
187 1X0P FAD 21.6783
188 3KP6 SAL 21.8543
189 5EY0 GTP 22
190 4RC8 STE 22.973
191 5Y02 HBX 23
192 4NSQ COA 23.6842
193 4XCP PLM 24.1176
194 4OGQ 7PH 24.1379
195 4OGQ 1O2 24.1379
196 4OGQ UMQ 24.1379
197 4OGQ SQD 24.1379
198 2Y69 CHD 24.4186
199 1HBK MYR 24.7191
200 5LX9 OLB 24.7423
201 2BYC FMN 25.5474
202 4RJD TFP 25.7576
203 5ZCO PEK 27.6596
204 5W97 CHD 27.6596
205 5ZCO CHD 27.6596
206 5Z84 CHD 27.6596
207 3X01 AMP 31
208 5MWE TCE 31.4286
209 4ZGM 32M 32.2581
210 2UW1 GVM 34
211 6FS0 E4W 44.186
212 5OCA 9QZ 47.4654
213 5LWY OLB 48.5981
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