Receptor
PDB id Resolution Class Description Source Keywords
2RIA 1.8 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE TRIMERIC NECK AND CARBOHYDRATE RECO DOMAIN OF HUMAN SURFACTANT PROTEIN D IN COMPLEX WITH D-GLYCM ANNO-HEPTOSE HOMO SAPIENS SURFACTANT PROTEIN; CARBOHYDRATE RECOGNITION; DOMAIN TRIMERIBINDING PROTEIN
Ref.: RECOGNITION OF HEPTOSES AND THE INNER CORE OF BACTE LIPOPOLYSACCHARIDES BY SURFACTANT PROTEIN D. BIOCHEMISTRY V. 47 710 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
289 A:356;
B:356;
C:356;
 Valid;
Valid;
Valid;
 none;
none;
none;
 ic50 = 2.7 mM
210.182 C7 H14 O7 C([C@...
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...
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: 289; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 289 1 1
2 GMH 1 1
3 GZL 0.862069 0.866667
4 M7P 0.511111 0.658537
5 GYE 0.428571 0.612903
Similar Ligands (3D)
Ligand no: 1; Ligand: 289; Similar ligands found: 189
No: Ligand Similarity coefficient
1 MAN 0.9506
2 MMA 0.9470
3 2M5 0.9409
4 GCU 0.9352
5 95Z 0.9318
6 GLC 0.9275
7 DMJ 0.9241
8 293 0.9230
9 BMA 0.9228
10 F34 0.9180
11 DBH 0.9153
12 IFL 0.9151
13 FRU 0.9143
14 GLF 0.9134
15 3HA 0.9130
16 IJZ 0.9094
17 ASC 0.9087
18 3F0 0.9080
19 3M0 0.9076
20 ASO 0.9073
21 SKM 0.9066
22 XX3 0.9045
23 SHA 0.9035
24 3IT 0.9035
25 BDP 0.9033
26 G2F 0.9031
27 ADA 0.9016
28 GCV 0.9014
29 BGC 0.9013
30 J9T 0.9012
31 ZB1 0.9006
32 GCB 0.9003
33 M6P 0.9002
34 TFU 0.9000
35 GLA 0.8999
36 GYP 0.8994
37 QIC 0.8992
38 4AA 0.8989
39 XXG 0.8986
40 FOT 0.8983
41 PA1 0.8970
42 SFU 0.8970
43 MNM 0.8969
44 3FH 0.8962
45 HJP 0.8954
46 BDF 0.8954
47 ZWZ 0.8952
48 EMZ 0.8948
49 HHA 0.8945
50 8S0 0.8941
51 SJ5 0.8940
52 CTS 0.8934
53 G3F 0.8929
54 GLT 0.8927
55 K5W 0.8927
56 JTH 0.8926
57 MZB 0.8917
58 LYL 0.8910
59 H62 0.8910
60 AMG 0.8907
61 K3Q 0.8902
62 SWA 0.8899
63 DHK 0.8897
64 TAG 0.8893
65 94B 0.8892
66 X6X 0.8889
67 GAF 0.8889
68 MT5 0.8887
69 CAX 0.8886
70 1SV 0.8880
71 4P0 0.8878
72 GAL 0.8871
73 SLC 0.8864
74 D1X 0.8861
75 FDK 0.8859
76 4ME 0.8853
77 FH2 0.8850
78 IFM 0.8843
79 9KH 0.8842
80 G4D 0.8826
81 2CZ 0.8825
82 IPD 0.8825
83 7MK 0.8825
84 HPT 0.8812
85 EVA 0.8811
86 BM3 0.8807
87 X05 0.8807
88 FE DB1 0.8799
89 SER PRO 0.8795
90 O2A 0.8794
91 GLG 0.8787
92 LAO 0.8787
93 ALA PRO 0.8786
94 X1P 0.8785
95 DHS 0.8785
96 TTL 0.8773
97 GTC 0.8772
98 261 0.8768
99 4NG 0.8766
100 LDP 0.8765
101 MA3 0.8763
102 XXR 0.8759
103 NOJ 0.8756
104 57O 0.8754
105 3R9 0.8750
106 OA3 0.8749
107 R9S 0.8745
108 NGT 0.8743
109 TSS 0.8738
110 GLO 0.8736
111 NGO 0.8735
112 94E 0.8734
113 HKD 0.8733
114 MIF 0.8732
115 PRZ 0.8729
116 CIT 0.8723
117 OHP 0.8722
118 HMQ 0.8718
119 LGC 0.8717
120 GL4 0.8714
121 SDD 0.8712
122 CIP 0.8708
123 2TQ 0.8708
124 2CL 0.8707
125 ISD 0.8706
126 KBG 0.8705
127 FLC 0.8703
128 B0D 0.8699
129 AH8 0.8693
130 H7Y 0.8691
131 SR4 0.8690
132 GOX 0.8688
133 M6D 0.8686
134 ARP 0.8686
135 9YT 0.8684
136 FX1 0.8680
137 GFP 0.8676
138 E35 0.8676
139 LNR 0.8675
140 G1P 0.8674
141 GDL 0.8672
142 WOO 0.8670
143 ZB6 0.8669
144 OXZ 0.8664
145 OMD 0.8663
146 55D 0.8655
147 DFB 0.8646
148 15A 0.8641
149 NDH 0.8640
150 ZXD 0.8640
151 JF4 0.8639
152 X8Z 0.8636
153 NDG 0.8634
154 NCT 0.8632
155 AFR 0.8631
156 7D2 0.8624
157 KG1 0.8621
158 92K 0.8613
159 G6P 0.8612
160 NAG 0.8608
161 F6P 0.8607
162 1SS 0.8603
163 948 0.8603
164 APS 0.8603
165 6R8 0.8603
166 LCN 0.8602
167 RAT 0.8592
168 7A2 0.8589
169 X09 0.8586
170 RNS 0.8586
171 AOS 0.8581
172 AHR 0.8580
173 A2G 0.8578
174 N8P 0.8577
175 8TW 0.8577
176 1LN 0.8575
177 KOJ 0.8574
178 GF1 0.8573
179 2LP 0.8562
180 RNT 0.8557
181 EDR 0.8551
182 PAU 0.8547
183 CDV 0.8542
184 M74 0.8535
185 EOL 0.8534
186 327 0.8533
187 BG6 0.8532
188 2FY 0.8524
189 XDE 0.8521
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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