Receptor
PDB id Resolution Class Description Source Keywords
3SCM 2.5 Å NON-ENZYME: IMMUNE CRYSTAL STRUCTURE OF AUTOREACTIVE-VALPHA14-VBETA6 NKT TCR IN WITH CD1D-ISOGLOBOTRIHEXOSYLCERAMIDE MUS MUSCULUS TERNARY COMPLEX IMMUNITY APC CELL SURFACE IMMUNE SYSTEM
Ref.: RECOGNITION OF BETA-LINKED SELF GLYCOLIPIDS MEDIATE NATURAL KILLER T CELL ANTIGEN RECEPTORS NAT.IMMUNOL. V. 12 827 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
LGN A:307;
Valid;
none;
submit data
1164.59 C62 H117 N O18 CCCCC...
NAG A:303;
A:304;
Part of Protein;
Part of Protein;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
NAG NAG A:305;
Part of Protein;
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
3SCM 2.5 Å NON-ENZYME: IMMUNE CRYSTAL STRUCTURE OF AUTOREACTIVE-VALPHA14-VBETA6 NKT TCR IN WITH CD1D-ISOGLOBOTRIHEXOSYLCERAMIDE MUS MUSCULUS TERNARY COMPLEX IMMUNITY APC CELL SURFACE IMMUNE SYSTEM
Ref.: RECOGNITION OF BETA-LINKED SELF GLYCOLIPIDS MEDIATE NATURAL KILLER T CELL ANTIGEN RECEPTORS NAT.IMMUNOL. V. 12 827 2011
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 199 families.
1 3QI9 - PII C42 H81 O13 P CCCCCCCCCC....
2 3SCM - LGN C62 H117 N O18 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: LGN; Similar ligands found: 54
No: Ligand ECFP6 Tc MDL keys Tc
1 LGN 1 1
2 IGC 1 1
3 BGC 18C GAL 0.913979 1
4 03F 0.72449 0.964286
5 EIS 0.647619 0.753425
6 SLF 0.647619 0.753425
7 BGC 18C GAL SIA 0.634328 0.903226
8 LAT SPH OCA 0.633027 0.931035
9 CIS 0.62963 0.753425
10 BGC 18C GAL NGA SIA GAL 0.594595 0.903226
11 SIA GAL BGC 16C 0.583942 0.903226
12 0SG 0.580357 0.739726
13 JLS 0.544643 0.929825
14 GGD 0.533898 0.789474
15 DB6 0.525424 0.929825
16 LAT SPH DAO 0.522124 0.896552
17 LAT SPH OLA 0.522124 0.896552
18 GM3 0.514019 0.928571
19 AGH 0.504587 0.912281
20 PBS 0.504587 0.912281
21 0SH 0.504587 0.912281
22 FEE 0.504587 0.912281
23 SFT 0.495798 0.753425
24 DMU 0.48 0.75
25 UMQ 0.48 0.75
26 LMU 0.48 0.75
27 LMT 0.48 0.75
28 GAL SPH EIC 0.475 0.896552
29 1PZ 0.456311 0.636364
30 1PX 0.456311 0.636364
31 ERA BGC GAL 0.442748 0.915254
32 C1Q 0.440945 0.913793
33 C8P 0.440945 0.913793
34 7LM 0.440945 0.913793
35 GAL SPH NER 0.440678 0.87931
36 1O2 0.435897 0.754386
37 C6Q 0.433071 0.913793
38 3TF 0.432203 0.754386
39 C8F 0.429688 0.854839
40 6UZ 0.424528 0.666667
41 SPL 0.424242 0.732143
42 16C 0.424242 0.732143
43 18C 0.424242 0.732143
44 GLA GAL NAG 0.420561 0.741379
45 NAG GAL GAL 0.420561 0.741379
46 MAN BMA NAG 0.420561 0.741379
47 1L2 0.419355 0.754386
48 GLA GAL GLC NBU 0.417476 0.696429
49 GLA EGA 0.408163 0.625
50 6CM 0.405941 0.732143
51 GAL NGA GLA BGC GAL 0.405172 0.741379
52 7LP 0.404412 0.868852
53 GLA GAL BGC 5VQ 0.401961 0.660714
54 GLC GAL NAG GAL 0.4 0.741379
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3SCM; Ligand: LGN; Similar sites found: 107
This union binding pocket(no: 1) in the query (biounit: 3scm.bio1) has 48 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3KFF XBT 0.03995 0.42309 3.7037
2 3KJM 245 0.0223 0.42569 4.0404
3 3B1M KRC 0.02884 0.40204 4.0404
4 4OAS 2SW 0.02358 0.42096 4.16667
5 4INW 1EY 0.03261 0.40757 4.28571
6 3LE7 ADE 0.01143 0.45494 5.30612
7 1TMX HGX 0.02456 0.40532 5.31401
8 1RL4 BL5 0.0191 0.40347 5.31915
9 1DZK PRZ 0.04132 0.40527 5.73248
10 3ROE THM 0.02444 0.4311 5.7971
11 3TDC 0EU 0.00001677 0.70352 6.06061
12 5V4R MGT 0.005847 0.48119 6.06061
13 3HR1 PF9 0.01235 0.41932 6.06061
14 4WX0 HXD 0.03121 0.4115 6.06061
15 5T7I LAT NAG GAL 0.005183 0.47677 6.45161
16 4QEK GLC 0.03816 0.40718 6.53061
17 5MBC FMN 0.04623 0.40277 6.53061
18 1IIU RTL 0.0238 0.40597 6.89655
19 4WN5 MVC 0.01149 0.4208 6.95652
20 4J25 OGA 0.01607 0.44556 6.9869
21 1NF8 BOG 0.003001 0.4966 7.07071
22 1LFO OLA 0.01166 0.42653 7.07071
23 1XIU REA 0.0197 0.41848 7.07071
24 4CCW VKC 0.04052 0.41813 7.07071
25 5CYV WCA 0.01083 0.41641 7.53425
26 3TL1 JRO 0.02513 0.43456 7.54717
27 4DOL PLM 0.006129 0.44357 7.72947
28 3KO0 TFP 0.02762 0.44086 7.92079
29 5K53 STE 0.005287 0.43977 8.01527
30 4I67 G G G RPC 0.005607 0.46165 8.04598
31 4UMJ BFQ 0.00358 0.48576 8.08081
32 1JL0 PUT 0.01445 0.44565 8.08081
33 5UGW GSH 0.01068 0.44287 8.08081
34 2QCX PF1 0.03832 0.42621 8.08081
35 2YJD YJD 0.03457 0.40923 8.08081
36 4BQY FNT 0.03009 0.40376 8.08081
37 4ZU4 4TG 0.0371 0.40767 8.10811
38 4MGA 27L 0.0141 0.45421 8.21256
39 5HCN DAO 0.03071 0.42961 8.21256
40 4TV1 36M 0.03181 0.42874 8.21256
41 5DXE EST 0.02652 0.41831 8.21256
42 4MGD 27N 0.04369 0.40701 8.21256
43 1TV5 N8E 0.01085 0.45519 8.27815
44 2BYC FMN 0.02927 0.41943 8.75912
45 2IYG FMN 0.03636 0.41442 8.87097
46 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.03896 0.41396 8.97959
47 4ZGM 32M 0.01717 0.45457 9.01639
48 4O1Z MXM 0.01307 0.41817 9.09091
49 1YRX FMN 0.03178 0.41109 9.09091
50 2OVD DAO 0.01579 0.44823 9.34066
51 1J78 VDY 0.03257 0.42417 9.38776
52 4RYV ZEA 0.04377 0.41346 9.67742
53 3TKA CTN 0.04224 0.409 9.79592
54 4ZSI GLP 0.03678 0.40786 9.94152
55 4ZSI 4R1 0.04059 0.40567 9.94152
56 5JSP DQY 0.0276 0.4359 9.95025
57 3WV6 GAL BGC 0.01782 0.43338 10.101
58 1SS4 CIT 0.01219 0.41222 10.101
59 1JAK IFG 0.04311 0.41047 10.101
60 3QRC SCR 0.001439 0.50137 10.1911
61 4WVW SLT 0.004254 0.49005 10.4167
62 4LWU 20U 0.02897 0.41632 10.5882
63 2VFT SOR 0.003671 0.47152 10.628
64 1XM4 PIL 0.03124 0.41792 10.9272
65 3RGA LSB 0.004013 0.4565 11.1111
66 5UC9 MYR 0.02837 0.42751 11.1111
67 2Z77 HE7 0.0009754 0.46342 11.5108
68 5E89 TD2 0.009016 0.4388 11.5108
69 5BVT PAM 0.02746 0.40567 11.9403
70 2HZQ STR 0.01464 0.44937 12.069
71 5ICK FEZ 0.03044 0.40623 12.0773
72 3B6C SDN 0.005665 0.47109 12.1212
73 3AJH BL3 0.03518 0.40314 12.1212
74 1QY1 PRZ 0.005673 0.4351 12.6437
75 1H4H XYP XYS XYP 0.04663 0.40258 13.0435
76 4IBF 1D5 0.03314 0.41328 13.1313
77 5FPX GLY SER SER HIS HIS HIS HIS HIS 0.01079 0.42817 13.2743
78 2VWA PTY 0.03126 0.43525 13.8614
79 4QVX 3CQ 0.01267 0.41881 14.1414
80 3ZLR X0B 0.005026 0.40264 14.1414
81 4Y24 TD2 0.01509 0.43853 14.2857
82 5N8V KZZ 0.03646 0.42144 14.4928
83 5CHR 4NC 0.004307 0.47803 14.5985
84 1I7M PUT 0.02661 0.42216 14.9254
85 3W54 RNB 0.03604 0.41138 15.1515
86 4F4S EFO 0.02386 0.43584 15.7895
87 1YUC EPH 0.007914 0.41466 15.9184
88 2ZHL NAG GAL GAL NAG 0.004603 0.46175 16.1616
89 4UCC ZKW 0.01457 0.46057 16.1616
90 5VRH OLB 0.01146 0.45565 16.1616
91 2HFN FMN 0.02978 0.40954 16.9935
92 2WPW ACO 0.0351 0.4089 17.1429
93 4YSX E23 0.01284 0.45107 17.1717
94 4V1T ADP 0.01943 0.41877 17.1875
95 4H6B 10X 0.03269 0.42409 17.4359
96 1ULE GLA GAL NAG 0.01018 0.46032 19.3333
97 5BVS EIC 0.02066 0.42061 19.697
98 2Y69 CHD 0.04549 0.41821 19.7674
99 5K52 OCD 0.007485 0.42949 20.202
100 4UA3 COA 0.01075 0.42513 21.2121
101 2ET1 GLV 0.009113 0.46196 22.2222
102 5LX9 OLB 0.01979 0.4249 23.1884
103 5MWE TCE 0.01797 0.44283 24.2857
104 4NB5 2JT 0.01079 0.42816 25.1462
105 3WMX THR 0.03094 0.43691 25.7143
106 1U0A BGC BGC BGC BGC 0.02665 0.41499 30.303
107 5LWY OLB 0.004548 0.45778 47.6636
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