Receptor
PDB id Resolution Class Description Source Keywords
3RUG 2.2 Å NON-ENZYME: IMMUNE CRYSTAL STRUCTURE OF VALPHA10-VBETA8.1 NKT TCR IN COMPLEX WI ALPHAGLUCOSYLCERAMIDE (C20:2) MUS MUSCULUS MOUSE CD1D MOUSE NKT IMMUNE SYSTEM
Ref.: A SEMI-INVARIANT V(ALPHA)10(+) T CELL ANTIGEN RECEP DEFINES A POPULATION OF NATURAL KILLER T CELLS WITH GLYCOLIPID ANTIGEN-RECOGNITION PROPERTIES NAT.IMMUNOL. V. 12 616 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DB6 A:303;
C:303;
Valid;
Valid;
none;
none;
Kd = 4.4 uM
770.131 C44 H83 N O9 CCCCC...
NAG A:304;
A:307;
C:304;
C:307;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
NAG NAG A:305;
C:305;
Part of Protein;
Part of Protein;
none;
none;
submit data
408.404 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3RUG 2.2 Å NON-ENZYME: IMMUNE CRYSTAL STRUCTURE OF VALPHA10-VBETA8.1 NKT TCR IN COMPLEX WI ALPHAGLUCOSYLCERAMIDE (C20:2) MUS MUSCULUS MOUSE CD1D MOUSE NKT IMMUNE SYSTEM
Ref.: A SEMI-INVARIANT V(ALPHA)10(+) T CELL ANTIGEN RECEP DEFINES A POPULATION OF NATURAL KILLER T CELLS WITH GLYCOLIPID ANTIGEN-RECOGNITION PROPERTIES NAT.IMMUNOL. V. 12 616 2011
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 199 families.
1 3RUG Kd = 4.4 uM DB6 C44 H83 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 65 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 43 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: DB6; Similar ligands found: 34
No: Ligand ECFP6 Tc MDL keys Tc
1 DB6 1 1
2 JLS 0.897727 1
3 PBS 0.816092 0.981481
4 AGH 0.816092 0.981481
5 0SH 0.816092 0.981481
6 FEE 0.775281 0.981481
7 GM3 0.677419 0.962963
8 C8P 0.669811 0.912281
9 C8F 0.669811 0.852459
10 C1Q 0.669811 0.912281
11 7LM 0.669811 0.912281
12 03F 0.663265 0.963636
13 C6Q 0.660377 0.912281
14 GAL SPH EIC 0.583333 0.894737
15 7LP 0.567797 0.866667
16 1L2 0.559633 0.781818
17 BGC 18C GAL 0.54955 0.929825
18 GAL SPH NER 0.54717 0.910714
19 QUV 0.536585 0.779412
20 IGC 0.525424 0.929825
21 LGN 0.525424 0.929825
22 CIS 0.517857 0.726027
23 QUY 0.517241 0.868852
24 EIS 0.504505 0.726027
25 SLF 0.504505 0.726027
26 GSL 0.490385 0.877193
27 1O2 0.486239 0.781818
28 3TF 0.481818 0.781818
29 0SG 0.436975 0.712329
30 GGD 0.422764 0.754386
31 LAT SPH OCA 0.421488 0.864407
32 SFT 0.421488 0.726027
33 LAT SPH DAO 0.40678 0.862069
34 LAT SPH OLA 0.40678 0.862069
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3RUG; Ligand: DB6; Similar sites found: 70
This union binding pocket(no: 1) in the query (biounit: 3rug.bio1) has 46 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1AUA BOG 0.007093 0.45992 4.14938
2 3RV5 DXC 0.02934 0.42737 4.49438
3 3JUQ AJD 0.01993 0.40165 5.05051
4 1DZK PRZ 0.01089 0.42914 5.09554
5 1RL4 BL5 0.005948 0.43923 5.31915
6 1IIU RTL 0.02263 0.40174 5.39216
7 1TMX HGX 0.01362 0.4119 5.80913
8 4QEK GLC 0.004901 0.44289 6.06061
9 3RGZ BLD 0.01233 0.43003 6.06061
10 4GGZ BTN 0.04774 0.4031 6.08696
11 3SLS 77D 0.02383 0.40913 6.22407
12 3P13 RIP 0.002434 0.48834 6.25
13 5AIG VPR 0.01827 0.43275 6.4
14 2V5E SCR 0.02001 0.41632 6.93069
15 1NF8 BOG 0.003874 0.48187 7.07071
16 1UNB AKG 0.001355 0.43821 7.07071
17 1UNB PN1 0.001509 0.43072 7.07071
18 2XEM SSV 0.01819 0.42882 7.07071
19 5C3R HMU 0.02572 0.4075 7.07071
20 5C3R AKG 0.02572 0.4075 7.07071
21 1Z03 OCH 0.02248 0.43204 7.35294
22 3TL1 JRO 0.008307 0.45611 7.54717
23 4DOL PLM 0.01943 0.41347 7.84314
24 4K6B GLU 0.04078 0.41752 8.07453
25 1JL0 PUT 0.006598 0.46766 8.08081
26 1SDW IYT 0.0168 0.42682 8.08081
27 2FR3 REA 0.0136 0.41785 8.08081
28 3UUA 0CZ 0.03057 0.40995 8.08081
29 1TV5 N8E 0.004626 0.47021 8.27815
30 2OVD DAO 0.005265 0.4692 8.79121
31 1J78 VDY 0.01286 0.44106 8.82353
32 2IYG FMN 0.02924 0.41429 8.87097
33 3PUR 2HG 0.002544 0.48648 8.9404
34 4O1Z MXM 0.006187 0.42762 9.09091
35 1YRX FMN 0.01466 0.42621 9.09091
36 1LFO OLA 0.004132 0.44248 9.375
37 3KMR EQN 0.01626 0.41414 10.7843
38 3TDC 0EU 0.03213 0.45315 10.7884
39 1QFT HSM 0.03063 0.40378 10.8571
40 5EXA 5SO 0.04615 0.41072 10.8696
41 3AVR OGA 0.02657 0.42974 10.9272
42 3GF4 U5P 0.01432 0.41677 11.1111
43 2HKA C3S 0.01989 0.40707 11.1111
44 3ZJX BOG 0.02311 0.43363 11.2745
45 4JH6 FCN 0.03081 0.42037 12.1212
46 4NFN 2KC 0.02092 0.41504 12.1212
47 3AJH BL3 0.01892 0.41099 12.1212
48 3OKI OKI 0.01881 0.40821 12.4464
49 3OF1 CMP 0.04215 0.40932 12.8631
50 3KYG 5GP 5GP 0.008389 0.42785 13.2159
51 2VWA PTY 0.01438 0.45755 13.8614
52 3OPT AKG 0.02008 0.43737 14.1414
53 5E89 TD2 0.01521 0.42193 14.7059
54 3PNA CMP 0.02091 0.42957 14.9351
55 3W54 RNB 0.01131 0.42491 15.1515
56 4KBA 1QM 0.03832 0.41517 15.1515
57 1OFL NGK GCD 0.006456 0.4602 15.1961
58 4F4S EFO 0.01124 0.44882 15.7895
59 2ZHL NAG GAL GAL NAG 0.002201 0.47246 16.1616
60 4UCC ZKW 0.006346 0.4649 16.1616
61 4GBD MCF 0.01653 0.40803 16.1616
62 2HI4 BHF 0.02539 0.40778 16.1616
63 4H69 10Y 0.02138 0.41788 16.4948
64 1JGS SAL 0.004312 0.43972 16.6667
65 4KVL PLM 0.01709 0.40468 19.1919
66 2Y69 CHD 0.04364 0.41047 22.973
67 1P1M MET 0.01638 0.40551 24.2424
68 1KDK DHT 0.002628 0.44128 28.2486
69 3OCP CMP 0.007891 0.44805 28.777
70 2C1Q BTN 0.0161 0.41744 29.3651
71 5NBW 8SK 0.03887 0.4078 50
Pocket No.: 2; Query (leader) PDB : 3RUG; Ligand: DB6; Similar sites found: 19
This union binding pocket(no: 2) in the query (biounit: 3rug.bio2) has 44 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1OI6 TMP 0.02083 0.42597 5.05051
2 3JUQ AKD 0.01665 0.40092 5.05051
3 2OVW CBI 0.04613 0.40916 6.06061
4 2YOO K2B 0.02494 0.40359 6.06061
5 4B7E OGA 0.04954 0.41223 7.07071
6 4J6C STR 0.03026 0.41918 7.94702
7 4I67 G G G RPC 0.04612 0.40564 8.04598
8 3MPB FRU 0.03791 0.40356 8.08081
9 2BYC FMN 0.04034 0.40218 8.75912
10 3P7N FMN 0.02063 0.40466 9.09091
11 5L9V OGA 0.04045 0.40869 9.12863
12 1EPB REA 0.01065 0.4279 10.101
13 1XM4 PIL 0.01722 0.42458 10.9272
14 3WDX BGC BGC GLC 0.01754 0.40796 11.2745
15 3KV4 OGA 0.04318 0.41543 18.1818
16 3KV5 OGA 0.02809 0.42051 19.1919
17 1W6P NDG GAL 0.03645 0.40294 20.8955
18 4IAW LIZ 0.004519 0.45901 21.2121
19 5LX9 OLB 0.03311 0.40657 25.9804
Feedback