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Receptor
PDB id Resolution Class Description Source Keywords
3HUJ 2.5 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF HUMAN CD1D-ALPHA-GALACTOSYLCERAMIDE IN WITH SEMI-INVARIANT NKT CELL RECEPTOR HOMO SAPIENS CD1D NKT T CELL RECEPTOR ALPHA-GALACTOSYLCERAMIDE PROTEINCOMPLEX CELL MEMBRANE DISULFIDE BOND ENDOSOME GLYCOPROTHOST-VIRUS INTERACTION IMMUNE RESPONSE IMMUNOGLOBULIN DOMINNATE IMMUNITY LYSOSOME MEMBRANE TRANSMEMBRANE DISEASEMUTATION GLYCATION MHC I PYRROLIDONE CARBOXYLIC ACID SEIMMUNE SYSTEM
Ref.: DIFFERENTIAL RECOGNITION OF CD1D-ALPHA-GALACTOSYL C BY THE V BETA 8.2 AND V BETA 7 SEMI-INVARIANT NKT T RECEPTORS IMMUNITY V. 31 47 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AGH A:3000;
C:3000;
 Valid;
Valid;
 none;
none;
 submit data
858.322 C50 H99 N O9 CCCCC...
MG H:1000;
 Part of Protein;
 none;
 submit data
24.305 Mg [Mg+2...
NAG A:2000;
 Invalid;
 none;
 submit data
221.208 C8 H15 N O6 CC(=O...
NAG NDG BMA C:1000;
 Invalid;
 none;
 submit data
570.545 n/a O=C(N...
NDG C:2000;
 Invalid;
 none;
 submit data
221.208 C8 H15 N O6 CC(=O...
NDG BMA A:1000;
 Invalid;
 none;
 submit data n/a n/a n/a n/a
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3HUJ 2.5 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF HUMAN CD1D-ALPHA-GALACTOSYLCERAMIDE IN WITH SEMI-INVARIANT NKT CELL RECEPTOR HOMO SAPIENS CD1D NKT T CELL RECEPTOR ALPHA-GALACTOSYLCERAMIDE PROTEINCOMPLEX CELL MEMBRANE DISULFIDE BOND ENDOSOME GLYCOPROTHOST-VIRUS INTERACTION IMMUNE RESPONSE IMMUNOGLOBULIN DOMINNATE IMMUNITY LYSOSOME MEMBRANE TRANSMEMBRANE DISEASEMUTATION GLYCATION MHC I PYRROLIDONE CARBOXYLIC ACID SEIMMUNE SYSTEM
Ref.: DIFFERENTIAL RECOGNITION OF CD1D-ALPHA-GALACTOSYL C BY THE V BETA 8.2 AND V BETA 7 SEMI-INVARIANT NKT T RECEPTORS IMMUNITY V. 31 47 2009
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 3HUJ - AGH C50 H99 N O9 CCCCCCCCCC....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 62 families.
1 4WO4 - JLS C48 H93 N O9 CCCCCCCCCC....
2 3RUG Kd = 4.4 uM DB6 C44 H83 N O9 CCCCCCCCCC....
3 3HUJ - AGH C50 H99 N O9 CCCCCCCCCC....
4 3QI9 - PII C42 H81 O13 P CCCCCCCCCC....
5 3SCM - LGN C62 H117 N O18 CCCCCCCCCC....
6 3QUZ Kd = 39.6 nM QUV C61 H107 N3 O9 CCCCCCCCCC....
7 3QUY Kd = 187 nM QUY C57 H104 N2 O9 CCCCCCCCCC....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 42 families.
1 4WO4 - JLS C48 H93 N O9 CCCCCCCCCC....
2 3RUG Kd = 4.4 uM DB6 C44 H83 N O9 CCCCCCCCCC....
3 3HUJ - AGH C50 H99 N O9 CCCCCCCCCC....
4 3QI9 - PII C42 H81 O13 P CCCCCCCCCC....
5 3SCM - LGN C62 H117 N O18 CCCCCCCCCC....
6 3QUZ Kd = 39.6 nM QUV C61 H107 N3 O9 CCCCCCCCCC....
7 3QUY Kd = 187 nM QUY C57 H104 N2 O9 CCCCCCCCCC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: AGH; Similar ligands found: 47
No: Ligand ECFP6 Tc MDL keys Tc
1 PBS 1 1
2 0SH 1 1
3 F61 1 1
4 AGH 1 1
5 FEE 0.945205 1
6 JLS 0.8875 0.981481
7 GM3 0.818182 0.981132
8 DB6 0.816092 0.981481
9 C1Q 0.788889 0.928571
10 C8P 0.788889 0.928571
11 7LM 0.788889 0.928571
12 C8F 0.788889 0.866667
13 C6Q 0.777778 0.928571
14 7LP 0.640777 0.881356
15 03F 0.633333 0.945455
16 QUV 0.616822 0.791045
17 QUY 0.6 0.883333
18 GSL 0.579545 0.892857
19 BGC 18C GAL 0.544554 0.912281
20 GAL SPH NER 0.510204 0.892857
21 IGC 0.504587 0.912281
22 LGN 0.504587 0.912281
23 SLF 0.49505 0.712329
24 EIS 0.49505 0.712329
25 CIS 0.480769 0.712329
26 LAT SPH DAO 0.470588 0.877193
27 LAT SPH OLA 0.470588 0.877193
28 HSJ 0.461538 0.754717
29 BNG 0.461538 0.754717
30 BOG 0.461538 0.754717
31 DGD 0.455446 0.75
32 KGM 0.448718 0.754717
33 B7G 0.448718 0.754717
34 1O2 0.445545 0.763636
35 3TF 0.441176 0.763636
36 JZR 0.435897 0.735849
37 GLC HEX 0.435897 0.735849
38 BHG 0.435897 0.735849
39 GAL SPH EIC 0.435185 0.877193
40 0SG 0.422018 0.69863
41 XNS 0.413793 0.722222
42 DR4 0.413793 0.722222
43 1L2 0.412844 0.763636
44 SFT 0.405405 0.712329
45 LAT SPH OCA 0.405405 0.847458
46 AFO 0.405063 0.690909
47 SER MAN 0.402439 0.678571
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3HUJ; Ligand: AGH; Similar sites found with APoc: 307
This union binding pocket(no: 1) in the query (biounit: 3huj.bio1) has 46 residues
No: Leader PDB Ligand Sequence Similarity
1 3KPE TM3 None
2 4WG0 CHD None
3 1UO5 PIH None
4 5HW4 SAM 3.22581
5 6CS8 F9Y 3.82775
6 4CJN MUR 4.0404
7 4WGF HX2 4.39024
8 5NCF 8T5 4.42478
9 4UMJ BFQ 4.47154
10 2GWH PCI 4.87805
11 4JZB P2H 5.05051
12 2RH1 CLR 5.05051
13 4K10 NI9 5.05051
14 2RH1 CAU 5.05051
15 5CPR 539 5.05051
16 4JZX 476 5.05051
17 3DXW ICC 5.26316
18 5HV7 RBL 5.28455
19 1ZDU P3A 5.30612
20 2XFE GAL GAL 5.35714
21 2D5X L35 5.67376
22 1TMX HGX 5.69106
23 2UXI G50 5.71429
24 3E70 GDP 5.74163
25 5OFW 9TW 5.8296
26 4EKQ NPO 5.88235
27 2Z77 HE7 5.98592
28 4DOO DAO 6.06061
29 3NZ1 3NY 6.06061
30 3SHZ 5CO 6.06061
31 4EE7 PIS 6.06061
32 5TZO 7V7 6.06061
33 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 6.08696
34 4MOB ADP 6.09756
35 5CYV WCA 6.16438
36 5CC2 CKA 6.2201
37 2WH8 II2 6.33803
38 5MBC FMN 6.50407
39 3QP8 HL0 6.52174
40 2J5B TYE 6.69014
41 4I90 CHT 6.69856
42 1KDK DHT 6.77966
43 5FUI APY 6.81818
44 1SDW IYT 7.04225
45 5KJW 53C 7.07071
46 1NF8 BOG 7.07071
47 5L2R MLA 7.07071
48 4UCC ZKW 7.07071
49 5X7Q GLC GLC 7.07071
50 1GT4 UNA 7.07071
51 5DQ8 FLF 7.07071
52 2AZ5 307 7.07071
53 1VCE SAH 7.07071
54 3V8S 0HD 7.07071
55 5V3Y 5V8 7.17703
56 2FP2 TSA 7.22892
57 5B0I BOG 7.39437
58 5NM7 GLY 7.39437
59 4IFP MAL 7.6555
60 1MID LAP 7.69231
61 1F52 ADP 7.72358
62 4OAR 2S0 7.75194
63 2O5L MNR 7.84314
64 1N8V BDD 8.03571
65 6CB2 OLC 8.08081
66 3W54 RNB 8.08081
67 3ROE THM 8.08081
68 3ZGJ RMN 8.08081
69 5OCG 9R5 8.08081
70 3FAL REA 8.08081
71 4NOS H4B 8.08081
72 3T03 3T0 8.08081
73 6ALW BMJ 8.08081
74 2WME NAP 8.08081
75 4RD0 GDP 8.08081
76 3GD9 GLC BGC BGC BGC 8.08081
77 4G2R H1L 8.08081
78 4QDC ASD 8.08081
79 1RDT L79 8.08081
80 3B99 U51 8.13397
81 4KBA 1QM 8.13397
82 1A78 TDG 8.20895
83 1F5F DHT 8.29268
84 4X8D AVI 8.4507
85 5OLK DTP 8.53659
86 4XR8 MAL 8.54271
87 2WLG SOP 8.61244
88 4CPH LH4 8.66142
89 4MTI 2DX 8.69565
90 2IYG FMN 8.87097
91 6GNO XDI 8.88889
92 4IA6 EIC 9.09091
93 2BHW NEX 9.09091
94 4YVN EBS 9.09091
95 6BMS POV 9.09091
96 3L1N PLM 9.09091
97 1Q7E MET 9.09091
98 3HYW DCQ 9.09091
99 3X01 AMP 9.09091
100 4NS3 NAD 9.09091
101 3E3U NVC 9.09091
102 1YRX FMN 9.09091
103 1M13 HYF 9.09091
104 2F99 AKV 9.15033
105 2OJW ADP 9.15493
106 3B6R ADP 9.15493
107 3KP6 SAL 9.27152
108 4V1F BQ1 9.30233
109 1U29 I3P 9.30233
110 3KMR EQN 9.3985
111 2HHP FLC 9.50704
112 2GBB CIT 9.61539
113 4XPL ACO 9.81595
114 4ZGM 32M 9.83607
115 3SQP 3J8 9.85915
116 1O6U PLM 10.0478
117 1OLM VTQ 10.0478
118 6AYI C3G 10.0503
119 5M36 9SZ 10.101
120 5M37 9SZ 10.101
121 6E1Q CFA 10.101
122 3CBC DBS 10.101
123 5H9O GLC 10.101
124 5LVP ATP 10.101
125 4D06 NAR 10.101
126 2GMH UQ5 10.101
127 3WG3 A2G GAL NAG FUC 10.1124
128 5H9P TD2 10.1266
129 2VL1 GLY GLY 10.1626
130 3H0L ADP 10.1626
131 2HFK E4H 10.1626
132 2FR3 REA 10.219
133 2VFT SOR 10.5263
134 1DKF BMS 10.6383
135 1UYY BGC BGC 10.687
136 3UW4 MAA CHG PRO 0DQ 10.8696
137 3DER ALA LYS 10.9155
138 5K52 OCD 10.9434
139 5UGW GSH 11.1111
140 4TV1 36M 11.1111
141 1XMY ROL 11.1111
142 4WOE ADP 11.1111
143 5K53 STE 11.1111
144 3G58 988 11.1111
145 4HBM 0Y7 11.1111
146 4MGA 27L 11.1111
147 1XM4 PIL 11.1111
148 1G51 AMP 11.1111
149 1GUX ASP LEU TYR CYS TYR GLU GLN LEU ASN 11.1111
150 1SLT NDG GAL 11.1111
151 3G4G D71 11.1111
152 1XMU ROF 11.1111
153 2C3Q GTX 11.1111
154 2QZO KN1 11.1111
155 4YEF 4CQ 11.236
156 1NU4 MLA 11.3402
157 1RQJ RIS 11.3712
158 3MBG FAD 11.5108
159 5HWV MBN 11.5385
160 3IWD M2T 11.7647
161 2NUN ADP 11.7886
162 5M6N 7H9 11.8644
163 1FWV SGA MAG FUC 11.9403
164 5FP4 YC8 11.9617
165 2YJD YJD 12.0833
166 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 12.1212
167 4YRI 4JH 12.1212
168 3OKI OKI 12.1212
169 1VHT BA3 12.3853
170 2POC BG6 12.4402
171 1ZB6 GST 12.4402
172 1DGH NDP 12.6016
173 1QY1 PRZ 12.6437
174 1QKQ MAN 12.6761
175 6EVN PRO PRO GLY PRO ALA GLY PRO PRO GLY 12.7451
176 3ZO7 K6H 12.766
177 3O55 FAD 12.8
178 3TDC 0EU 13.0081
179 2ZJ3 G6P 13.0081
180 4YSX E23 13.1313
181 5AZC PGT 13.1313
182 5DEQ ARA 13.1313
183 4FE2 AIR 13.1313
184 3PGU OLA 13.1313
185 3BP1 GUN 13.1313
186 2ZSC BTN 13.1313
187 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU 13.1579
188 1R6N 434 13.2701
189 6CGN DA 13.3971
190 4D52 GIV 13.4146
191 4D52 GXL 13.4146
192 5T7I LAT NAG GAL 13.5484
193 4RLT FSE 13.6054
194 6CAY ERG 13.6095
195 6BYM HC3 13.7931
196 1ZPD CIT 13.8211
197 5CHR 4NC 13.8686
198 2XG5 EC5 13.8728
199 2XG5 EC2 13.8728
200 6FA4 D1W 13.8728
201 1YP0 PEF 13.8756
202 3V78 ET 13.9423
203 2JC9 ADN 14.0845
204 5L7G LYS SER LEU LEU GLN GLN LEU LEU THR GLU 14.0845
205 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 14.1414
206 1W6U HXC 14.1414
207 3F8C HT1 14.2857
208 1M48 FRG 14.2857
209 2OO0 PLP 14.3541
210 5XJ7 87O 14.4279
211 1KPH 10A 15.0407
212 1KPG 16A 15.0407
213 2Y7P SAL 15.1376
214 1XZ3 ICF 15.1515
215 1J78 VDY 15.1515
216 5H9Y BGC BGC BGC BGC 15.1515
217 4F4S EFO 15.7895
218 5CX6 CDP 15.8451
219 3EFS BTN 15.8798
220 1TV5 N8E 16.1616
221 5KR7 6X9 16.1616
222 3G5K BB2 16.1616
223 5YRV 5AD 16.1972
224 1GPM AMP 16.1972
225 1Y4Z PCI 16.2602
226 1I7M CG 16.4179
227 4RC8 STE 16.6667
228 3TL1 JRO 16.9811
229 2QHV OC9 17.1717
230 2QHS OCA 17.1717
231 4DR9 BB2 17.1717
232 1NQ7 HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU 17.2131
233 3A16 PXO 17.2249
234 3ZXE PGZ 17.2932
235 5Y4R C2E 17.931
236 5IM3 DTP 18.1818
237 5OQW A4E 18.1818
238 1ZED PNP 18.1818
239 3CM2 X23 18.1818
240 5C83 4YN 18.1818
241 1VPV PLM 18.1818
242 6BMM OLB 18.1818
243 4AMV F6R 18.1818
244 2Y69 CHD 18.6047
245 2GQS C2R 19.1388
246 2NPA MMB 19.1919
247 5A4W QCT 19.1919
248 5XLY C2E 19.5489
249 3RMK BML 19.9187
250 3OYW TDG 20.1493
251 1GZW GAL BGC 20.1493
252 2VSL MAA LYS PRO PHE 20.8333
253 3ZF8 GDP 21.2121
254 4O4Z N2O 21.4286
255 5X3R 7Y3 21.4634
256 5Z84 CHD 21.7391
257 5ZCO CHD 21.7391
258 2DYR PGV 21.7391
259 5ZCO PGV 21.7391
260 5W97 CHD 21.7391
261 5ZCO PEK 21.7391
262 5Z84 PGV 21.7391
263 5Z84 PEK 21.7391
264 2DYR TGL 21.7391
265 4I67 G G G RPC 21.8391
266 1I0B PEL 22.0096
267 2P5B OGA 22.0096
268 4M51 BEZ 22.0096
269 4H6B 10X 22.0513
270 2HZL PYR 22.2222
271 1TO9 HMH 22.2222
272 5UC9 MYR 22.2222
273 2OS2 OGA 22.488
274 1LSH PLD 23.2323
275 1U6R ADP 23.2323
276 2H8H H8H 23.2323
277 5VNF VAL THR SER VAL VAL 23.2394
278 5B4B LP5 23.7903
279 4Y24 TD2 24.026
280 4OGQ 1O2 24.1379
281 4OGQ 7PH 24.1379
282 3N7S 3N7 24.3478
283 1ZEI CRS 24.5283
284 5TVF CGQ 24.7059
285 1X0P FAD 25.2525
286 5LX9 OLB 25.8373
287 5W7B MYR 26.2626
288 3KRO PPV 26.2626
289 1H8S AIC 27.2358
290 5LRT ADP 28.2828
291 3BEJ MUF 28.2828
292 1M2Z BOG 28.5714
293 5Y02 MXN 28.972
294 3K56 IS3 31.3131
295 2UW1 GVM 32.3232
296 5VRH OLB 32.3232
297 2BCG GER 35.9223
298 5C1M OLC 36.8
299 5C1M CLR 36.8
300 5C1M 4VO 36.8
301 5LWY OLB 42.8571
302 2CJU PHX 43.8017
303 43CA NPO 45.2991
304 5OCA 9QZ 46.083
305 1MEX RAC 46.4789
306 2YKL NLD 46.7593
307 3WFD AXO 47.4178
Pocket No.: 2; Query (leader) PDB : 3HUJ; Ligand: AGH; Similar sites found with APoc: 134
This union binding pocket(no: 2) in the query (biounit: 3huj.bio2) has 48 residues
No: Leader PDB Ligand Sequence Similarity
1 4UBS DIF 3.34928
2 1P0Z FLC 3.81679
3 5X80 SAL 5
4 3RGA LSB 5.05051
5 3LDW IPE 5.05051
6 3BJC WAN 6.06061
7 4O1Z MXM 6.06061
8 3KYQ DPV 6.06061
9 4B1V LAB 6.06061
10 4MYD 164 6.06061
11 1UNB PN1 6.06061
12 1OGX EQU 6.10687
13 2CDO GAL AAL GAL AAL GAL AAL 6.875
14 4NKW PLO 6.91057
15 3PUR 2HG 7.04225
16 6C1R EFD 7.07071
17 3HOK Q80 7.07071
18 4DE3 DN8 7.17703
19 6B04 C6J 7.17703
20 4I94 ANP 7.17703
21 4DDY DN6 7.17703
22 1OW4 2AN 7.75194
23 4JGX PLM 7.75194
24 2HJ3 FAD 8
25 3RDE OYP 8.08081
26 5HCN DAO 8.13397
27 5UV1 0FV 8.4507
28 2Q4G CIT 8.53659
29 3ZPG 5GP 8.63874
30 3EE4 MYR 8.94309
31 4H6U ACO 9
32 3HP9 CF1 9.09091
33 1TW4 CHD 9.09091
34 3W5N RAM 9.09091
35 5JBX MLI 9.09091
36 5A86 D7E 9.09091
37 6BMS PLM 9.09091
38 1XX4 BAM 9.34959
39 4MRP GSH 9.56938
40 2YOO K2B 9.56938
41 1DTL BEP 9.93789
42 4YEE 4CQ 10
43 5TFZ 7BC 10.101
44 4HN1 TYD 10.101
45 2Q8G AZX 10.101
46 3HR1 PF9 10.101
47 4XCP PLM 10.101
48 5B25 4QJ 10.101
49 3GYT DL4 10.101
50 1UBY DMA 10.101
51 5T9C G3P 10.4478
52 1H4H XYP XYS XYP 10.5263
53 1DKF OLA 10.6383
54 1FK5 OLA 10.7527
55 4B1M FRU FRU 10.8108
56 1YYE 196 10.8209
57 5F8F SFG 11.1111
58 1JAY F42 11.1111
59 4TUZ 36J 11.1111
60 5HYR EST 11.1111
61 4MGD 27N 11.1111
62 4MG7 27H 11.1111
63 4MG8 27J 11.1111
64 5DXG EST 11.1111
65 3UUD EST 11.1111
66 5DX3 EST 11.1111
67 5WGD EST 11.1111
68 5DXE EST 11.1111
69 3RY9 1CA 11.1111
70 2QA8 GEN 11.1111
71 5WGQ EST 11.1111
72 1U3R 338 12.0332
73 3LE7 ADE 12.1212
74 2BP1 FLC 12.1212
75 2CIX CEJ 12.1212
76 1ULE GLA GAL NAG 12.1212
77 6D5J FV4 12.1212
78 6D5H FV7 12.1212
79 6D5L FW7 12.1212
80 6D56 FVM 12.1212
81 6D5E FVG 12.1212
82 6D59 FVJ 12.1212
83 6BVM EBV 12.1212
84 6BVK EAV 12.1212
85 6D5M FW4 12.1212
86 6D55 FWA 12.1212
87 6D5G FVD 12.1212
88 3N0Y APC 12.1212
89 2HFN FMN 12.4183
90 1JNQ EGT 12.4402
91 4XB4 45D 12.5
92 1KGI T4A 12.5984
93 3NB0 G6P 12.9187
94 3JRS A8S 12.9808
95 3V2Q PLM 13.3333
96 2I6A 5I5 13.3803
97 1SBR VIB 13.5
98 4M26 AKG 14.1414
99 4OCT AKG 14.1414
100 6C0B PAM 14.1414
101 1HBK MYR 14.6067
102 3SAO NKN 15
103 2QJY UQ2 15.1515
104 4Q0A 4OA 15.1515
105 1U1J MET 15.1515
106 4YUS FMN 15.1515
107 1LN1 DLP 15.311
108 2VDY HCY 15.4472
109 1XXR MAN 15.528
110 2ET1 GLV 16.1616
111 1J3R 6PG 16.1616
112 1R89 CTP 16.1616
113 1I7M PUT 16.4179
114 1CZA ADP 18.1818
115 2ZHL NAG GAL GAL NAG 18.1818
116 1QCI ADE 19.1388
117 3L0E G58 19.1919
118 5TDU PCR 19.9187
119 1W6P NDG GAL 20.1493
120 1W6O LAT 20.1493
121 1ELW GLY PRO THR ILE GLU GLU VAL ASP 21.2121
122 2DYS PGV 21.7391
123 1T0S BML 22.093
124 2QCX PF1 22.2222
125 4PAB THG 22.2222
126 2VQ5 HBA 23.2323
127 1ZGA HMK 23.2323
128 4DXJ 0M9 25.8373
129 4DXJ IPE 25.8373
130 6A5Y 9CR 28.2828
131 5Y02 HBX 28.972
132 2XN5 FUN 30.303
133 5XQW 8EU 45.0237
134 2IBZ UQ6 48.5981
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