Receptor
PDB id Resolution Class Description Source Keywords
3G84 2.3 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE TRIMERIC NECK AND CARBOHYDRATE RECO DOMAIN OF R343V MUTANT OF HUMAN SURFACTANT PROTEIN D IN COMA LPHA 1,2 DIMANNOSE. HOMO SAPIENS SURFACTANT PROTEIN CARBOHYDRATE RECOGNITION DOMAIN TRIMERICOLLAGEN EXTRACELLULAR MATRIX GASEOUS EXCHANGE GLYCOPROTHYDROXYLATION LECTIN SECRETED SURFACE FILM SUGAR BINDIN
Ref.: RECOGNITION OF MANNOSYLATED LIGANDS AND INFLUENZA A HUMAN SURFACTANT PROTEIN D: CONTRIBUTIONS OF AN EXT SITE AND RESIDUE 343. BIOCHEMISTRY V. 48 3335 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:401;
A:402;
A:403;
B:401;
B:402;
B:403;
C:401;
C:402;
C:403;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
MAN MAN F:1;
E:1;
D:1;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
326.298 n/a O(C1C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2GGX 1.9 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE TRIMER NECK AND CARBOHYDRATE RECOGN DOMAIN OF HUMAN SURFACTANT PROTEIN D IN COMPLEX WITH P-NITRM ALTOSIDE HOMO SAPIENS PROTEIN-CARBOHYDRATE LIGAND COMPLEX SUGAR BINDING PROTEIN
Ref.: CONTRIBUTIONS OF PHENYLALANINE 335 TO LIGAND RECOGN HUMAN SURFACTANT PROTEIN D: RING INTERACTIONS WITH LIGANDS J.BIOL.CHEM. V. 281 18008 2006
Members (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 2RIA ic50 = 2.7 mM 289 C7 H14 O7 C([C@H]([C....
2 3G81 - MMA C7 H14 O6 CO[C@@H]1[....
3 2ORJ - BM3 C8 H15 N O6 CC(=O)N[C@....
4 2GGX ic50 = 0.32 mM NPJ C18 H25 N O13 c1cc(ccc1[....
5 2RIE - 293 C7 H14 O6 C1[C@H]([C....
6 2RIC - GMH GMH n/a n/a
7 3G84 - MAN MAN n/a n/a
8 2ORK ic50 = 1.4 mM IPD C6 H11 O9 P [C@H]1([C@....
9 2OS9 - INS C6 H12 O6 C1(C(C(C(C....
10 2GGU ic50 = 0.94 mM GLC GLC GLC n/a n/a
11 3G83 - MAN MAN n/a n/a
12 2RID ic50 = 1.7 mM 291 C11 H19 N O8 C=CCO[C@@H....
70% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 214 families.
1 3IKR - MAN C6 H12 O6 C([C@@H]1[....
2 1PWB - GLC C6 H12 O6 C([C@@H]1[....
3 3IKQ - MAN C6 H12 O6 C([C@@H]1[....
4 3IKP - IPD C6 H11 O9 P [C@H]1([C@....
5 5OXS - K5B GMH GMH GLC n/a n/a
6 5OXR - K5B GMH GMH n/a n/a
7 3IKN - GAL C6 H12 O6 C([C@@H]1[....
8 4DN8 - BMA C6 H12 O6 C([C@@H]1[....
9 2RIA ic50 = 2.7 mM 289 C7 H14 O7 C([C@H]([C....
10 3G81 - MMA C7 H14 O6 CO[C@@H]1[....
11 2ORJ - BM3 C8 H15 N O6 CC(=O)N[C@....
12 2GGX ic50 = 0.32 mM NPJ C18 H25 N O13 c1cc(ccc1[....
13 2RIE - 293 C7 H14 O6 C1[C@H]([C....
14 2RIC - GMH GMH n/a n/a
15 3G84 - MAN MAN n/a n/a
16 2ORK ic50 = 1.4 mM IPD C6 H11 O9 P [C@H]1([C@....
17 2OS9 - INS C6 H12 O6 C1(C(C(C(C....
18 2GGU ic50 = 0.94 mM GLC GLC GLC n/a n/a
19 3G83 - MAN MAN n/a n/a
20 2RID ic50 = 1.7 mM 291 C11 H19 N O8 C=CCO[C@@H....
50% Homology Family (49)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 181 families.
1 3IKR - MAN C6 H12 O6 C([C@@H]1[....
2 1PWB - GLC C6 H12 O6 C([C@@H]1[....
3 3IKQ - MAN C6 H12 O6 C([C@@H]1[....
4 3IKP - IPD C6 H11 O9 P [C@H]1([C@....
5 5OXS - K5B GMH GMH GLC n/a n/a
6 5OXR - K5B GMH GMH n/a n/a
7 3IKN - GAL C6 H12 O6 C([C@@H]1[....
8 2MSB Ki = 1.3 mM NAG BMA MAN MAN MAN MAN MAN n/a n/a
9 4DN8 - BMA C6 H12 O6 C([C@@H]1[....
10 1AFB - NGA C8 H15 N O6 CC(=O)N[C@....
11 1KWW - MFU C7 H14 O5 C[C@H]1[C@....
12 1KX0 - MAN MAN n/a n/a
13 1KWY - MAN MAN n/a n/a
14 1FIH - NGA C8 H15 N O6 CC(=O)N[C@....
15 4KMB - MAG FUC G4S n/a n/a
16 1BCH - NGA C8 H15 N O6 CC(=O)N[C@....
17 1KWV - NAG C8 H15 N O6 CC(=O)N[C@....
18 1BCJ Kd = 0.2 mM NGA C8 H15 N O6 CC(=O)N[C@....
19 1KWX - MFB C7 H14 O5 C[C@H]1[C@....
20 1KWU - MMA C7 H14 O6 CO[C@@H]1[....
21 1KWZ - MAN MAN n/a n/a
22 1AFA - MBG C7 H14 O6 CO[C@H]1[C....
23 3KMB - FUC C6 H12 O5 C[C@H]1[C@....
24 2KMB - NAG GAL SIA FUC n/a n/a
25 2RIA ic50 = 2.7 mM 289 C7 H14 O7 C([C@H]([C....
26 3G81 - MMA C7 H14 O6 CO[C@@H]1[....
27 2ORJ - BM3 C8 H15 N O6 CC(=O)N[C@....
28 2GGX ic50 = 0.32 mM NPJ C18 H25 N O13 c1cc(ccc1[....
29 2RIE - 293 C7 H14 O6 C1[C@H]([C....
30 2RIC - GMH GMH n/a n/a
31 3G84 - MAN MAN n/a n/a
32 2ORK ic50 = 1.4 mM IPD C6 H11 O9 P [C@H]1([C@....
33 2OS9 - INS C6 H12 O6 C1(C(C(C(C....
34 2GGU ic50 = 0.94 mM GLC GLC GLC n/a n/a
35 3G83 - MAN MAN n/a n/a
36 2RID ic50 = 1.7 mM 291 C11 H19 N O8 C=CCO[C@@H....
37 6RYM - NDG C8 H15 N O6 CC(=O)N[C@....
38 6RYN - GN1 C8 H16 N O9 P CC(=O)N[C@....
39 1KZD - NAG C8 H15 N O6 CC(=O)N[C@....
40 1RDI Ki = 8.8 mM MFU C7 H14 O5 C[C@H]1[C@....
41 1RDL Ki = 5.7 mM MMA C7 H14 O6 CO[C@@H]1[....
42 1KZC - MAN C6 H12 O6 C([C@@H]1[....
43 1KZA - MAN C6 H12 O6 C([C@@H]1[....
44 1KZE - MAN C6 H12 O6 C([C@@H]1[....
45 1RDN Ki = 14.4 mM NDG C8 H15 N O6 CC(=O)N[C@....
46 1RDK Ki = 114 mM GAL C6 H12 O6 C([C@@H]1[....
47 1KZB - MAN C6 H12 O6 C([C@@H]1[....
48 1RDJ Ki = 21.7 mM MFB C7 H14 O5 C[C@H]1[C@....
49 1RDM Ki = 5.7 mM MMA C7 H14 O6 CO[C@@H]1[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: MAN MAN; Similar ligands found: 76
No: Ligand ECFP6 Tc MDL keys Tc
1 MAN MAN 1 1
2 GAL FUC 0.686275 0.970588
3 7D1 MAN 0.584906 0.942857
4 GLC IFM 0.571429 0.727273
5 BQZ 0.5 0.909091
6 ISX 0.5 0.761905
7 GAL GLA 0.5 0.941176
8 XYP IOB BGC 0.486111 0.780488
9 3CU GLC 0.483333 0.615385
10 RZM 0.482143 0.688889
11 MBG GLA 0.481481 0.888889
12 MAN G63 0.47541 0.6875
13 G2F BGC BGC BGC BGC BGC 0.46875 0.868421
14 MAN BMA BMA 0.467742 0.942857
15 NOJ GLC 0.466667 0.733333
16 XYS GLC GLC 0.462687 0.914286
17 LG9 GLC 0.460317 0.603774
18 GYP 0.458333 0.857143
19 MMA 0.458333 0.857143
20 AMG 0.458333 0.857143
21 MBG 0.458333 0.857143
22 GLC BGC BGC BGC 0.457627 0.941176
23 BGC BGC BGC BGC BGC BGC BGC 0.457627 0.941176
24 BGC BGC BGC BGC BGC BGC 0.457627 0.941176
25 BGC BGC BGC BGC BGC 0.457627 0.941176
26 BGC BGC BGC 0.457627 0.941176
27 MBG GAL 0.45614 0.888889
28 MGL GAL 0.45614 0.888889
29 BGC GLA GAL 0.454545 0.941176
30 IFM BGC 0.45 0.711111
31 RR7 GLC 0.448276 0.888889
32 XYS XYS AHR 0.447761 0.864865
33 XYP XYP AHR 0.447761 0.864865
34 MAN MAN BMA 0.446154 0.942857
35 NAG BMA 0.446154 0.6875
36 NAG GAL 0.444444 0.695652
37 BDF GLC 0.444444 0.916667
38 MAN MNM 0.442623 0.666667
39 NOY BGC 0.442623 0.666667
40 GLC DMJ 0.442623 0.733333
41 GLC GLC GLC GLC BGC GLC GLC 0.440678 0.941176
42 MAN BMA BMA BMA BMA BMA BMA 0.440678 0.941176
43 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.440678 0.941176
44 CJX 0.435484 0.680851
45 5QP 0.433333 0.941176
46 FRU GLC 0.433333 0.794872
47 BGC OXZ 0.42623 0.666667
48 9MR 0.42623 0.744186
49 XYP XYP AHR XYP 0.424658 0.864865
50 BGC FUC GAL 0.424242 0.914286
51 GLC BGC FUC GAL 0.424242 0.914286
52 GLC G6P 0.423729 0.744186
53 AHR FUB 0.423077 0.805556
54 A2G GAL 0.421875 0.695652
55 FUC GAL 0.416667 0.885714
56 XYS AHR XYP XYP XYP 0.416667 0.864865
57 BMA MAN MAN 0.415385 0.941176
58 GLC 7LQ 0.412698 0.885714
59 BGC XGP 0.412698 0.744186
60 GCU BGC 0.412698 0.861111
61 ABL 0.412698 0.666667
62 XYP XYP XYP AHR 0.410959 0.864865
63 MAN IPD MAN 0.409836 0.744186
64 DGO MAN 0.409836 0.914286
65 FRU BMA 0.409836 0.794872
66 GLC U8V 0.409836 0.864865
67 GAL FUC GAL 0.409091 0.914286
68 XYP XYP XYP AHR XYP 0.407895 0.864865
69 GDQ GLC 0.40625 0.666667
70 BGC GAL GLA 0.40625 0.941176
71 GLC GLC GLC 0.405797 0.942857
72 IPD MAN 0.403226 0.697674
73 GLC EDO GLC 0.403226 0.888889
74 GAL SO4 GAL 0.402985 0.627451
75 G2F SHG BGC BGC 0.4 0.842105
76 MGC GAL 0.4 0.666667
Similar Ligands (3D)
Ligand no: 1; Ligand: MAN MAN; Similar ligands found: 31
No: Ligand Similarity coefficient
1 MMA MAN 0.9802
2 DMJ MAN 0.9768
3 ZEL MAN 0.9637
4 MAN GLC 0.9624
5 MAN IFM 0.9559
6 BMA MAN 0.9430
7 GLC GLC 0.9325
8 MSX MAN 0.9314
9 IFM MAN 0.9292
10 MMA LDY 0.9235
11 GLC FRU 0.9233
12 DGO Z61 0.9199
13 Z5L MAN 0.9176
14 BMA GLA 0.9175
15 MAN MVL 0.9160
16 BGC GLC 0.9156
17 GLA GLC 0.9115
18 GLC GLA 0.9098
19 GMH GMH 0.9093
20 XMM 0.9053
21 TW7 GLC 0.8865
22 BGC GLA 0.8855
23 BMA MVL 0.8770
24 SER MAN 0.8766
25 MVL BMA 0.8669
26 GLA BEZ 0.8637
27 RNK 0.8586
28 EGA GLA 0.8573
29 DTK 0.8572
30 BGC BGC 0.8559
31 SGC GLC 0.8509
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2GGX; Ligand: NPJ; 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: 2ggx.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2GGX; Ligand: NPJ; 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: 2ggx.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2GGX; Ligand: NPJ; Similar sites found with APoc: 1
This union binding pocket(no: 3) in the query (biounit: 2ggx.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 2OX9 NAG FUC GAL 43.5714
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