Receptor
PDB id Resolution Class Description Source Keywords
2GGX 1.9 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE TRIMER NECK AND CARBOHYDRATE RECOGNITION DOMAIN OF HUMAN SURFACTANT PROTEIN D IN C OMPLEX WITH P-NITROPHENYL MALTOSIDE HOMO SAPIENS PROTEIN-CARBOHYDRATE LIGAND COMPLEX SUGAR BINDING PROTEIN
Ref.: CONTRIBUTIONS OF PHENYLALANINE 335 TO LIGAND RECOGNITION BY HUMAN SURFACTANT PROTEIN D: RING INTERACTIONS WITH SP-D LIGANDS J.BIOL.CHEM. V. 281 18008 2006
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...
NPJ A:700;
B:700;
C:700;
Valid;
Valid;
Valid;
none;
none;
none;
ic50 = 0.32 mM
463.39 C18 H25 N O13 c1cc(...
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 RECOGNITION DOMAIN OF HUMAN SURFACTANT PROTEIN D IN C OMPLEX WITH P-NITROPHENYL MALTOSIDE HOMO SAPIENS PROTEIN-CARBOHYDRATE LIGAND COMPLEX SUGAR BINDING PROTEIN
Ref.: CONTRIBUTIONS OF PHENYLALANINE 335 TO LIGAND RECOGNITION BY HUMAN SURFACTANT PROTEIN D: RING INTERACTIONS WITH SP-D 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 1256 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 MLR C18 H32 O16 C([C@@H]1[....
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 (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 196 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 3IKN - GAL C6 H12 O6 C([C@@H]1[....
6 4DN8 - BMA C6 H12 O6 C([C@@H]1[....
7 2RIA ic50 = 2.7 mM 289 C7 H14 O7 C([C@H]([C....
8 3G81 - MMA C7 H14 O6 CO[C@@H]1[....
9 2ORJ - BM3 C8 H15 N O6 CC(=O)N[C@....
10 2GGX ic50 = 0.32 mM NPJ C18 H25 N O13 c1cc(ccc1[....
11 2RIE - 293 C7 H14 O6 C1[C@H]([C....
12 2RIC - GMH GMH n/a n/a
13 3G84 - MAN MAN n/a n/a
14 2ORK ic50 = 1.4 mM IPD C6 H11 O9 P [C@H]1([C@....
15 2OS9 - INS C6 H12 O6 C1(C(C(C(C....
16 2GGU ic50 = 0.94 mM MLR C18 H32 O16 C([C@@H]1[....
17 3G83 - MAN MAN n/a n/a
18 2RID ic50 = 1.7 mM 291 C11 H19 N O8 C=CCO[C@@H....
50% Homology Family (42)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 171 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 3IKN - GAL C6 H12 O6 C([C@@H]1[....
6 2MSB Ki = 1.3 mM NAG BMA MAN MAN MAN MAN MAN n/a n/a
7 4DN8 - BMA C6 H12 O6 C([C@@H]1[....
8 1AFB - NGA C8 H15 N O6 CC(=O)N[C@....
9 1KWW - MFU C7 H14 O5 C[C@H]1[C@....
10 1KX0 - MAN MAN n/a n/a
11 1KWY - MAN MAN n/a n/a
12 1FIH - NGA C8 H15 N O6 CC(=O)N[C@....
13 4KMB - G4S MAG FUC n/a n/a
14 1BCH - NGA C8 H15 N O6 CC(=O)N[C@....
15 1KWV - NAG C8 H15 N O6 CC(=O)N[C@....
16 1KWX - MFB C7 H14 O5 C[C@H]1[C@....
17 1KWU - MMA C7 H14 O6 CO[C@@H]1[....
18 1KWZ - MAN MAN n/a n/a
19 1AFA - MBG C7 H14 O6 CO[C@H]1[C....
20 3KMB - FUC C6 H12 O5 C[C@H]1[C@....
21 2KMB - SIA GAL MAG FUC n/a n/a
22 2RIA ic50 = 2.7 mM 289 C7 H14 O7 C([C@H]([C....
23 3G81 - MMA C7 H14 O6 CO[C@@H]1[....
24 2ORJ - BM3 C8 H15 N O6 CC(=O)N[C@....
25 2GGX ic50 = 0.32 mM NPJ C18 H25 N O13 c1cc(ccc1[....
26 2RIE - 293 C7 H14 O6 C1[C@H]([C....
27 2RIC - GMH GMH n/a n/a
28 3G84 - MAN MAN n/a n/a
29 2ORK ic50 = 1.4 mM IPD C6 H11 O9 P [C@H]1([C@....
30 2OS9 - INS C6 H12 O6 C1(C(C(C(C....
31 2GGU ic50 = 0.94 mM MLR C18 H32 O16 C([C@@H]1[....
32 3G83 - MAN MAN n/a n/a
33 2RID ic50 = 1.7 mM 291 C11 H19 N O8 C=CCO[C@@H....
34 1KZD - NAG C8 H15 N O6 CC(=O)N[C@....
35 1RDI Ki = 8.8 mM MFU C7 H14 O5 C[C@H]1[C@....
36 1RDL Ki = 5.7 mM MMA C7 H14 O6 CO[C@@H]1[....
37 1KZC - MAN C6 H12 O6 C([C@@H]1[....
38 1KZA - MAN C6 H12 O6 C([C@@H]1[....
39 1RDK Ki = 114 mM GAL C6 H12 O6 C([C@@H]1[....
40 1KZB - MAN C6 H12 O6 C([C@@H]1[....
41 1RDJ Ki = 21.7 mM MFB C7 H14 O5 C[C@H]1[C@....
42 1RDM Ki = 5.7 mM MMA C7 H14 O6 CO[C@@H]1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NPJ; Similar ligands found: 128
No: Ligand ECFP6 Tc MDL keys Tc
1 NPJ 1 1
2 RCB 0.967742 1
3 NBZ GLA 0.725806 0.962264
4 GAL NPO 0.725806 0.962264
5 147 0.725806 0.962264
6 PNG 0.725806 0.962264
7 PNW 0.725806 0.962264
8 MBE 0.725806 0.962264
9 PNA 0.725806 0.962264
10 GLA NPO 0.725806 0.962264
11 KHP 0.677419 0.890909
12 GAL A2G NPO 0.6 0.84127
13 NPO A2G GAL 0.6 0.84127
14 NGB 0.6 1
15 NSQ 0.555556 0.710145
16 NIN MBF BMA BMA 0.54023 0.854839
17 4MU BGC BGC 0.535714 0.6
18 NDG BDP BDP NPO NDG 0.530612 0.828125
19 4MU BGC BGC BGC BGC 0.529412 0.6
20 PNJ 0.527778 0.87931
21 6Y2 0.523256 0.828125
22 LAT GLA 0.523077 0.622642
23 MMA MAN 0.522388 0.6
24 DR5 0.522388 0.6
25 GAA 0.520548 0.944444
26 DCB 0.517647 0.854839
27 LEC 0.512821 0.809524
28 6ZC 0.512821 0.809524
29 GNS BDP GNS BDP GNS BDP NPO 0.510204 0.736111
30 LAM 0.505495 0.946429
31 GLC BGC BGC 0.485714 0.622642
32 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.485714 0.622642
33 BGC GLC GLC GLC GLC 0.485714 0.622642
34 B4G 0.485714 0.622642
35 BMA BMA BMA BMA BMA 0.485714 0.622642
36 CEX 0.485714 0.622642
37 BGC BGC BGC BGC BGC BGC 0.485714 0.622642
38 CE6 0.485714 0.622642
39 MLR 0.485714 0.622642
40 GLA GAL GLC 0.485714 0.622642
41 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.485714 0.622642
42 GAL GAL GAL 0.485714 0.622642
43 CEY 0.485714 0.622642
44 MT7 0.485714 0.622642
45 GLC BGC BGC BGC BGC 0.485714 0.622642
46 GLC GLC GLC GLC GLC GLC GLC GLC 0.485714 0.622642
47 BMA BMA BMA BMA BMA BMA 0.485714 0.622642
48 MTT 0.485714 0.622642
49 GLC GLC GLC GLC GLC GLC GLC 0.485714 0.622642
50 BMA MAN BMA 0.485714 0.622642
51 BGC GLC GLC GLC GLC GLC GLC 0.485714 0.622642
52 GLC GLC BGC 0.485714 0.622642
53 MAN MAN BMA BMA BMA BMA 0.485714 0.622642
54 CTT 0.485714 0.622642
55 CT3 0.485714 0.622642
56 GLC GLC BGC GLC GLC GLC GLC 0.485714 0.622642
57 GLC BGC GLC 0.485714 0.622642
58 BGC BGC BGC GLC 0.485714 0.622642
59 GLC BGC BGC BGC BGC BGC 0.485714 0.622642
60 MAN BMA BMA 0.485714 0.622642
61 BGC GLC GLC GLC 0.485714 0.622642
62 DXI 0.485714 0.622642
63 CTR 0.485714 0.622642
64 CE8 0.485714 0.622642
65 BMA BMA BMA 0.485714 0.622642
66 GLC GLC GLC GLC GLC 0.485714 0.622642
67 CE5 0.485714 0.622642
68 GLC GAL GAL 0.485714 0.622642
69 BGC GLC GLC 0.485714 0.622642
70 MAN BMA BMA BMA BMA 0.485714 0.622642
71 GLA EGA 0.478873 0.6
72 MAL EDO 0.472222 0.6
73 LEC NGA 0.47191 0.828125
74 BGC GAL 0.470588 0.622642
75 GLC BGC 0.470588 0.622642
76 GLC GAL 0.470588 0.622642
77 GLA GAL 0.470588 0.622642
78 56N 0.470588 0.622642
79 BMA BMA 0.470588 0.622642
80 MAB 0.470588 0.622642
81 LBT 0.470588 0.622642
82 BMA GAL 0.470588 0.622642
83 CBI 0.470588 0.622642
84 LAT 0.470588 0.622642
85 GLA GLA 0.470588 0.622642
86 GAL GLC 0.470588 0.622642
87 CBK 0.470588 0.622642
88 GAL BGC 0.470588 0.622642
89 MAL MAL 0.470588 0.611111
90 XTG 0.470588 0.896552
91 MAL 0.470588 0.622642
92 B2G 0.470588 0.622642
93 N9S 0.470588 0.622642
94 BGC BMA 0.470588 0.622642
95 BGC GLC 0.470588 0.622642
96 3XN 0.465909 0.8125
97 GAT 0.463768 0.690909
98 GLC GLC XYS 0.4625 0.611111
99 BMA BMA BMA BMA BMA BMA MAN 0.459459 0.611111
100 BGC BGC GLC 0.459459 0.622642
101 MAN BMA BMA BMA BMA BMA 0.459459 0.611111
102 GAL PHB 0.458333 0.611111
103 GNS BDP GNS IDS GNS BDP NPO 0.446429 0.736111
104 3X8 0.445946 0.6
105 MVP 0.44 0.606557
106 LAG 0.439024 0.6875
107 GLA MBG 0.434783 0.6
108 BGC BGC BGC BGC BGC BGC BGC BGC 0.43038 0.622642
109 BGC BGC BGC BGC 0.43038 0.622642
110 145 0.423077 0.927273
111 OXZ BGC BGC 0.419753 0.655738
112 GLC GLC GLC GLC GLC GLC 0.419753 0.622642
113 GLC GLC XYP 0.419753 0.622642
114 HNW 0.415584 0.618182
115 GLA GAL GAL 0.415584 0.622642
116 GLA GAL BGC 0.415584 0.622642
117 SOR GLC GLC 0.414634 0.611111
118 MAN MAN 0.414286 0.622642
119 2M4 0.414286 0.622642
120 BGC BGC 0.414286 0.622642
121 GLA BEZ 0.405063 0.62963
122 SOR GLC GLC GLC 0.404762 0.611111
123 BMA BMA GLA BMA BMA 0.404762 0.622642
124 GAL BGC NAG GAL 0.404494 0.606557
125 GAL BGC BGC XYS 0.402299 0.6
126 GLO GLC GLC 0.402299 0.6
127 4MU MAN MAN 0.402174 0.6
128 BGC BGC ZZ1 0.402174 0.6
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2GGX; Ligand: NPJ; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2GGX; Ligand: NPJ; Similar sites found: 33
This union binding pocket(no: 2) in the query (biounit: 2ggx.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WVW SLT 0.01717 0.4006 2.08333
2 5H9Q TD2 0.01143 0.40877 3.22581
3 4JAW NGT GAL 0.007879 0.42244 4.375
4 1UPR 4IP 0.0169 0.40069 4.87805
5 2AAZ UMP 0.008837 0.41933 5
6 1IMB LIP 0.01268 0.41153 5
7 4ISK UMP 0.006577 0.42126 6.25
8 1ZPR UMP 0.00809 0.41686 6.25
9 2A9W UMP 0.005633 0.41652 6.25
10 1JG0 UMP 0.006021 0.41493 6.25
11 1SYN UMP 0.01076 0.41289 6.25
12 1NCE UMP 0.01345 0.40818 6.25
13 1TSD UMP 0.01445 0.40384 6.25
14 1DDU DDU 0.005079 0.40354 6.25
15 3BLI ACO 0.02803 0.40374 6.875
16 3A5Z KAA 0.02806 0.40722 8.125
17 1KAP GLY SER ASN SER 0.01661 0.40438 8.125
18 1BB6 UMG 0.008248 0.43059 8.52713
19 1G1T SIA GAL MAG FUC 0.0000001232 0.65828 17.1975
20 3ALT MLB 0.0004572 0.46599 24.2038
21 3WH2 FLC 0.00001403 0.54188 26.5306
22 1SL6 GAL NDG FUC 0.00000001135 0.61224 28.125
23 5JQ1 ZPF 0.00000005679 0.63859 28.9655
24 1SL4 MAN MAN MAN MAN 0.000001565 0.61598 29.6774
25 4WQQ MAN 0.00000001598 0.72084 29.7872
26 4KZV TRE 0.000000122 0.57016 29.8507
27 4ZES MMA 0.00000001836 0.77682 34.6939
28 1K9J NAG MAN MAN MAN NAG 0.0000006047 0.63103 35.2518
29 3P7G MAN 0.00000003308 0.70082 35.6164
30 1JZN BGC GAL 0.00000002357 0.72745 37.037
31 3VYK MMA MAN NAG MAN NAG NAG 0.00000003464 0.67989 37.9845
32 1TLG GAL 0.000001264 0.61928 41.6
33 2OX9 GAL NAG FUC 0.00000005603 0.69676 43.5714
Pocket No.: 3; Query (leader) PDB : 2GGX; Ligand: NPJ; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2ggx.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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