Receptor
PDB id Resolution Class Description Source Keywords
5WKG 2.06 Å NON-ENZYME: IMMUNE CRYSTAL STRUCTURE OF HUMAN CD1B IN COMPLEX WITH PA HOMO SAPIENS ANTIGEN PRESENTING MOLECULE PA PHOSPHOLIPID MHC CD1B IMSYSTEM
Ref.: A MOLECULAR BASIS OF HUMAN T CELL RECEPTOR AUTOREAC TOWARD SELF-PHOSPHOLIPIDS. SCI IMMUNOL V. 2 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:414;
A:416;
B:202;
A:415;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
35.453 Cl [Cl-]
CUY A:412;
Valid;
Atoms found LESS than expected: % Diff = 0.182;
submit data
621.115 C42 H84 O2 CCCCC...
NAG A:408;
Invalid;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
NA B:201;
Part of Protein;
none;
submit data
22.99 Na [Na+]
NAG FUC NAG FUC BMA MAN MAN A:401;
Invalid;
none;
submit data n/a n/a n/a n/a
IOD B:203;
A:419;
A:418;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
126.904 I [I-]
PEG A:413;
Invalid;
none;
submit data
106.12 C4 H10 O3 C(COC...
NAG FUC A:409;
Invalid;
none;
submit data
367.351 n/a O=C(N...
EDO A:417;
Invalid;
none;
submit data
62.068 C2 H6 O2 C(CO)...
D21 A:411;
Valid;
none;
submit data
674.929 C37 H71 O8 P CCCCC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5WL1 1.38 Å NON-ENZYME: IMMUNE CRYSTAL STRUCTURE OF HUMAN CD1B IN COMPLEX WITH PG HOMO SAPIENS ANTIGEN PRESENTING MOLECULE PG PHOSPHOLIPID MHC CD1B IMSYSTEM
Ref.: A MOLECULAR BASIS OF HUMAN T CELL RECEPTOR AUTOREAC TOWARD SELF-PHOSPHOLIPIDS. SCI IMMUNOL V. 2 2017
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 208 families.
1 5WKE - P50 C40 H76 N O9 P CCCCCCCCCC....
2 1GZQ - PII C42 H81 O13 P CCCCCCCCCC....
3 5L2J - 70E C42 H82 O8 CCCCCCCCCC....
4 5WL1 - D3D C40 H77 O10 P CCCCCCCCCC....
5 5WKG - CUY C42 H84 O2 CCCCCCCCCC....
6 2H26 - 6UL C40 H80 O2 CCCCCCCCCC....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 62 families.
1 5WKE - P50 C40 H76 N O9 P CCCCCCCCCC....
2 1GZQ - PII C42 H81 O13 P CCCCCCCCCC....
3 5L2J - 70E C42 H82 O8 CCCCCCCCCC....
4 5WL1 - D3D C40 H77 O10 P CCCCCCCCCC....
5 5WKG - CUY C42 H84 O2 CCCCCCCCCC....
6 2H26 - 6UL C40 H80 O2 CCCCCCCCCC....
7 5C9J - STE C18 H36 O2 CCCCCCCCCC....
8 3L9R - L9Q C41 H80 N O8 P CCCCCCCCCC....
50% Homology Family (33)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 42 families.
1 5WKE - P50 C40 H76 N O9 P CCCCCCCCCC....
2 1GZQ - PII C42 H81 O13 P CCCCCCCCCC....
3 5L2J - 70E C42 H82 O8 CCCCCCCCCC....
4 5WL1 - D3D C40 H77 O10 P CCCCCCCCCC....
5 5WKG - CUY C42 H84 O2 CCCCCCCCCC....
6 2H26 - 6UL C40 H80 O2 CCCCCCCCCC....
7 3GMM - PLM C16 H32 O2 CCCCCCCCCC....
8 3G08 Kd = 6.843 nM FEE C39 H77 N O9 CCCCCCCCCC....
9 3MA7 - CD4 C65 H126 O17 P2 CCCCCCCCCC....
10 1Z5L - PBS C32 H63 N O9 CCCCCCCCCC....
11 5TW5 - PLM C16 H32 O2 CCCCCCCCCC....
12 3ILQ Kd = 6.2 uM 1O2 C43 H80 O10 CCCCCCCCCC....
13 3GMR - PLM C16 H32 O2 CCCCCCCCCC....
14 3T1F - 3TF C43 H80 O10 CCCCCCCCCC....
15 3GMQ - PLM C16 H32 O2 CCCCCCCCCC....
16 6BMH - F61 C35 H69 N O9 CCCCCCCCCC....
17 2AKR - CIS C48 H91 N O11 S CCCCCCCCCC....
18 3GMP - PBS C32 H63 N O9 CCCCCCCCCC....
19 3AU1 - ERA BGC GAL n/a n/a
20 3GMN - PLM C16 H32 O2 CCCCCCCCCC....
21 5TW2 - 7LP C34 H58 N2 O10 CCCCCCCC(=....
22 3GML - PLM C16 H32 O2 CCCCCCCCCC....
23 2Q7Y - IGC C44 H81 N O18 CCCCCCCCCC....
24 6BMK - F57 C31 H61 O8 P CCCCCCCCCC....
25 3ILP - 1L2 C45 H80 O10 CCCCCCCC/C....
26 3GMO - PLM C16 H32 O2 CCCCCCCCCC....
27 2FIK - PLM C16 H32 O2 CCCCCCCCCC....
28 1ONQ - SLF C42 H81 N O11 S CCCCCCCCCC....
29 4X6E - 42H C26 H53 N O7 P CCCCCCCC/C....
30 4X6F - 3XU C47 H94 N2 O6 P CCCCCCCCCC....
31 4F7E - 0SH C40 H79 N O9 CCCCCCCCCC....
32 5C9J - STE C18 H36 O2 CCCCCCCCCC....
33 3L9R - L9Q C41 H80 N O8 P CCCCCCCCCC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: CUY; Similar ligands found: 31
No: Ligand ECFP6 Tc MDL keys Tc
1 6UL 1 1
2 CUY 1 1
3 CNS 1 1
4 T80 0.5625 0.777778
5 GYM 0.510638 0.606061
6 1QW 0.510638 0.606061
7 TGL 0.5 0.724138
8 56S 0.488372 0.791667
9 DDR 0.461538 0.677419
10 DGA 0.461538 0.677419
11 FAW 0.461538 0.677419
12 L2C 0.461538 0.677419
13 TWN 0.457627 0.65625
14 G2A 0.456522 0.625
15 2JT 0.456522 0.625
16 DKA 0.435897 0.68
17 X90 0.435897 0.68
18 TDA 0.435897 0.68
19 DCR 0.435897 0.68
20 EW8 0.435897 0.68
21 11A 0.435897 0.68
22 F23 0.435897 0.68
23 KNA 0.435897 0.68
24 DAO 0.435897 0.68
25 PLM 0.435897 0.68
26 MYR 0.435897 0.68
27 F15 0.435897 0.68
28 STE 0.435897 0.68
29 OCA 0.410256 0.68
30 VA 0.408163 0.954545
31 LBR 0.40678 0.606061
Ligand no: 2; Ligand: D21; Similar ligands found: 101
No: Ligand ECFP6 Tc MDL keys Tc
1 D21 1 1
2 3PH 0.847458 0.976744
3 7PH 0.847458 0.976744
4 LPP 0.847458 0.976744
5 F57 0.847458 0.976744
6 6PH 0.847458 0.976744
7 7P9 0.833333 0.976744
8 PD7 0.783333 0.976744
9 LOP 0.75 0.792453
10 L9Q 0.75 0.792453
11 6OU 0.75 0.792453
12 D3D 0.739726 0.913043
13 PGW 0.739726 0.913043
14 M7U 0.735294 0.976744
15 DR9 0.72973 0.913043
16 PGV 0.72973 0.913043
17 44E 0.721311 0.976744
18 PCW 0.72 0.732143
19 P6L 0.72 0.913043
20 OZ2 0.710526 0.913043
21 P50 0.710526 0.823529
22 ZPE 0.706667 0.792453
23 B7N 0.701299 0.84
24 PX8 0.692308 0.909091
25 PX2 0.692308 0.909091
26 PIE 0.670886 0.784314
27 P3A 0.670886 0.87234
28 POV 0.666667 0.690909
29 L9R 0.666667 0.690909
30 NKP 0.661765 0.954545
31 GP7 0.654321 0.792453
32 PSC 0.638554 0.732143
33 CD4 0.633803 0.931818
34 TGL 0.633333 0.674419
35 8PE 0.625 0.773585
36 PTY 0.625 0.773585
37 PEV 0.625 0.773585
38 PEF 0.625 0.773585
39 PEH 0.625 0.773585
40 PGT 0.616438 0.891304
41 9PE 0.616438 0.773585
42 LHG 0.616438 0.891304
43 PEE 0.616438 0.759259
44 PEK 0.609756 0.792453
45 CDL 0.60274 0.844444
46 HGP 0.6 0.714286
47 6PL 0.6 0.714286
48 HGX 0.6 0.714286
49 LIO 0.6 0.714286
50 PC7 0.6 0.714286
51 P5S 0.6 0.788462
52 PLD 0.6 0.714286
53 3PE 0.586667 0.698113
54 PII 0.584416 0.82
55 PIZ 0.580247 0.857143
56 DLP 0.569767 0.690909
57 PIF 0.56962 0.84
58 CN3 0.56962 0.931818
59 T7X 0.568182 0.84
60 IP9 0.567901 0.857143
61 EPH 0.566667 0.792453
62 OLC 0.558824 0.652174
63 OLB 0.558824 0.652174
64 XP5 0.552632 0.714286
65 PCF 0.551282 0.672727
66 PC1 0.551282 0.672727
67 MC3 0.551282 0.672727
68 52N 0.548781 0.84
69 PIO 0.548781 0.84
70 L2C 0.545455 0.681818
71 FAW 0.545455 0.681818
72 DGA 0.545455 0.681818
73 DDR 0.545455 0.681818
74 CN6 0.544304 0.931818
75 AGA 0.538462 0.851064
76 MVC 0.536232 0.652174
77 PGK 0.535714 0.836735
78 NKO 0.529412 0.931818
79 NKN 0.529412 0.931818
80 42H 0.52439 0.736842
81 PCK 0.523256 0.677966
82 78N 0.521739 0.652174
83 78M 0.521739 0.652174
84 44G 0.52 0.891304
85 DGG 0.517241 0.836735
86 S12 0.512195 0.788462
87 PSF 0.506494 0.788462
88 LBR 0.493151 0.630435
89 PDK 0.459184 0.672131
90 G2A 0.453125 0.644444
91 2JT 0.453125 0.644444
92 SQD 0.449438 0.6
93 GYM 0.426471 0.630435
94 1QW 0.426471 0.630435
95 OPC 0.419355 0.719298
96 LP3 0.414634 0.719298
97 1PZ 0.414634 0.727273
98 1PX 0.414634 0.727273
99 LAP 0.414634 0.719298
100 LPC 0.414634 0.719298
101 PGM 0.405063 0.829787
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5WL1; Ligand: CUY; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5wl1.bio1) has 67 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5WL1; Ligand: D3D; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5wl1.bio1) has 67 residues
No: Leader PDB Ligand Sequence Similarity
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