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 1256 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 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: AGH; Similar ligands found: 46
No: Ligand ECFP6 Tc MDL keys Tc
1 AGH 1 1
2 PBS 1 1
3 0SH 1 1
4 FEE 0.945205 1
5 JLS 0.8875 0.981481
6 GM3 0.818182 0.981132
7 DB6 0.816092 0.981481
8 C8F 0.788889 0.866667
9 C8P 0.788889 0.928571
10 7LM 0.788889 0.928571
11 C1Q 0.788889 0.928571
12 C6Q 0.777778 0.928571
13 7LP 0.640777 0.881356
14 03F 0.633333 0.945455
15 QUV 0.616822 0.791045
16 QUY 0.6 0.883333
17 GSL 0.579545 0.892857
18 BGC 18C GAL 0.544554 0.912281
19 GAL SPH NER 0.510204 0.892857
20 IGC 0.504587 0.912281
21 LGN 0.504587 0.912281
22 EIS 0.49505 0.712329
23 SLF 0.49505 0.712329
24 CIS 0.480769 0.712329
25 LAT SPH OLA 0.470588 0.877193
26 LAT SPH DAO 0.470588 0.877193
27 BOG 0.461538 0.754717
28 BNG 0.461538 0.754717
29 HSJ 0.461538 0.754717
30 DGD 0.455446 0.75
31 B7G 0.448718 0.754717
32 KGM 0.448718 0.754717
33 1O2 0.445545 0.763636
34 3TF 0.441176 0.763636
35 GLC HEX 0.435897 0.735849
36 HEX GLC 0.435897 0.735849
37 BHG 0.435897 0.735849
38 JZR 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 LAT SPH OCA 0.405405 0.847458
45 SFT 0.405405 0.712329
46 AFO 0.405063 0.690909
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3HUJ; Ligand: AGH; Similar sites found: 62
This union binding pocket(no: 1) in the query (biounit: 3huj.bio1) has 46 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO5 PIH 0.03331 0.43356 None
2 5HW4 SAM 0.02388 0.40066 3.22581
3 1A5Z FBP 0.0453 0.40956 3.44828
4 4CJN MUR 0.0147 0.42616 4.0404
5 1TMX HGX 0.004855 0.43244 5.69106
6 2Z77 HE7 0.001421 0.44983 5.98592
7 1KDK DHT 0.01407 0.40849 6.77966
8 1NF8 BOG 0.001833 0.50354 7.07071
9 4UCC ZKW 0.02038 0.4459 7.07071
10 2AZ5 307 0.02724 0.40628 7.07071
11 4IFP MAL 0.04298 0.41242 7.6555
12 3ZGJ RMN 0.01685 0.43904 8.08081
13 3ROE THM 0.04495 0.41135 8.08081
14 3W54 RNB 0.02675 0.40666 8.08081
15 1RDT L79 0.02693 0.40088 8.08081
16 4KBA 1QM 0.04339 0.40214 8.13397
17 4MTI 2DX 0.04138 0.41716 8.69565
18 2IYG FMN 0.03798 0.40833 8.87097
19 3L1N PLM 0.02532 0.42915 9.09091
20 3HYW DCQ 0.03699 0.41962 9.09091
21 3E3U NVC 0.042 0.40287 9.09091
22 3B6R ADP 0.02897 0.40798 9.15493
23 3KP6 SAL 0.01318 0.44687 9.27152
24 3KMR EQN 0.02225 0.40761 9.3985
25 4XPL ACO 0.03583 0.40043 9.81595
26 2V5E SCR 0.00716 0.45506 9.90099
27 2GMH UQ5 0.02387 0.40066 10.101
28 2FR3 REA 0.02459 0.40553 10.219
29 2VFT SOR 0.02279 0.42361 10.5263
30 1XM4 PIL 0.01869 0.42442 11.1111
31 1XMU ROF 0.03132 0.40941 11.1111
32 2NUN ADP 0.03753 0.41567 11.7886
33 3OKI OKI 0.01632 0.4111 12.1212
34 3TDC 0EU 0.00272 0.53839 13.0081
35 4FE2 AIR 0.02147 0.425 13.1313
36 2XG5 EC5 0.006177 0.45058 13.8728
37 2XG5 EC2 0.006177 0.45058 13.8728
38 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.00503 0.48289 14.1414
39 1KPG 16A 0.01633 0.41715 15.0407
40 2Y7P SAL 0.01195 0.44735 15.1376
41 1J78 VDY 0.03868 0.41494 15.1515
42 4F4S EFO 0.02621 0.42831 15.7895
43 1TV5 N8E 0.004501 0.47087 16.1616
44 3G5K BB2 0.04743 0.40014 16.1616
45 1I7M CG 0.01872 0.43218 16.4179
46 3TL1 JRO 0.03246 0.42311 16.9811
47 2QHV OC9 0.02629 0.42413 17.1717
48 2QHS OCA 0.04001 0.41053 17.1717
49 4DR9 BB2 0.03487 0.40702 17.1717
50 1NQ7 HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU 0.013 0.4408 17.2131
51 4AMV F6R 0.04032 0.40076 18.1818
52 2Y69 CHD 0.02662 0.42802 18.6047
53 2NPA MMB 0.01833 0.40596 19.1919
54 1GZW GAL BGC 0.02988 0.41511 20.1493
55 4I67 G G G RPC 0.03356 0.41463 21.8391
56 4H6B 10X 0.001283 0.48455 22.0513
57 2QCX PF1 0.02259 0.43444 22.2222
58 5UC9 MYR 0.02618 0.42423 22.2222
59 5LX9 OLB 0.0434 0.40213 25.8373
60 1H8S AIC 0.04891 0.40932 27.2358
61 2CJU PHX 0.04332 0.41844 43.8017
62 5OCA 9QZ 0.005908 0.46524 46.083
Pocket No.: 2; Query (leader) PDB : 3HUJ; Ligand: AGH; Similar sites found: 31
This union binding pocket(no: 2) in the query (biounit: 3huj.bio2) has 48 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4UBS DIF 0.04507 0.41504 3.34928
2 3RGA LSB 0.006959 0.4405 5.05051
3 4O1Z MXM 0.01279 0.41479 6.06061
4 3KYQ DPV 0.04978 0.41412 6.06061
5 4B1V LAB 0.03724 0.41373 6.06061
6 1UNB PN1 0.007372 0.40488 6.06061
7 2CDO GAL AAL GAL AAL GAL AAL 0.01541 0.43216 6.875
8 3PUR 2HG 0.03937 0.42172 7.04225
9 3ZPG 5GP 0.02456 0.42918 8.63874
10 1YRX FMN 0.005363 0.45007 9.09091
11 1XX4 BAM 0.02001 0.44511 9.34959
12 2YOO K2B 0.01469 0.41787 9.56938
13 1JL0 PUT 0.03207 0.42039 9.7561
14 4XCP PLM 0.03479 0.42106 10.101
15 1FK5 OLA 0.01823 0.40501 10.7527
16 4MGA 27L 0.02716 0.43687 11.1111
17 4MGD 27N 0.02817 0.41332 11.1111
18 4MG8 27J 0.03224 0.41031 11.1111
19 3RY9 1CA 0.03247 0.40407 11.1111
20 3LE7 ADE 0.006245 0.4685 12.1212
21 3N0Y APC 0.01649 0.40441 12.1212
22 1JNQ EGT 0.03191 0.40445 12.4402
23 4OCT AKG 0.03562 0.41477 14.1414
24 4Q0A 4OA 0.01278 0.42078 15.1515
25 1I7M PUT 0.03266 0.41889 16.4179
26 2ZHL NAG GAL GAL NAG 0.02734 0.41737 18.1818
27 1W6P NDG GAL 0.04521 0.40768 20.1493
28 1W6O LAT 0.02804 0.40566 20.1493
29 1ELW GLY PRO THR ILE GLU GLU VAL ASP 0.04146 0.40785 21.2121
30 1M2Z BOG 0.02702 0.43281 28.5714
31 2XN5 FUN 0.03085 0.41814 30.303
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