Receptor
PDB id Resolution Class Description Source Keywords
1RDL 1.7 Å NON-ENZYME: BINDING MANNOSE-BINDING PROTEIN, SUBTILISIN DIGEST FRAGMENT COMPLEX WITH ALPHA-METHYL-D-MANNOPYRANOSIDE (0.2 M) RATTUS RATTUS C-TYPE LECTIN CALCIUM-BINDING PROTEIN
Ref.: STRUCTURAL ANALYSIS OF MONOSACCHARIDE RECOGNITION BY RAT LIVER MANNOSE-BINDING PROTEIN. J.BIOL.CHEM. V. 271 663 1996
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA 1:2;
1:227;
2:2;
2:227;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
CL 1:3;
Invalid;
none;
submit data
35.453 Cl [Cl-]
MMA 1:1;
2:1;
Valid;
Valid;
none;
none;
Ki = 5.7 mM
194.182 C7 H14 O6 CO[C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1RDL 1.7 Å NON-ENZYME: BINDING MANNOSE-BINDING PROTEIN, SUBTILISIN DIGEST FRAGMENT COMPLEX WITH ALPHA-METHYL-D-MANNOPYRANOSIDE (0.2 M) RATTUS RATTUS C-TYPE LECTIN CALCIUM-BINDING PROTEIN
Ref.: STRUCTURAL ANALYSIS OF MONOSACCHARIDE RECOGNITION BY RAT LIVER MANNOSE-BINDING PROTEIN. J.BIOL.CHEM. V. 271 663 1996
Members (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 473 families.
1 1KZD - NAG C8 H15 N O6 CC(=O)N[C@....
2 1RDI Ki = 8.8 mM MFU C7 H14 O5 C[C@H]1[C@....
3 1RDL Ki = 5.7 mM MMA C7 H14 O6 CO[C@@H]1[....
4 1KZC - MAN C6 H12 O6 C([C@@H]1[....
5 1KZA - MAN C6 H12 O6 C([C@@H]1[....
6 1KZE - MAN C6 H12 O6 C([C@@H]1[....
7 1RDN Ki = 14.4 mM NDG C8 H15 N O6 CC(=O)N[C@....
8 1RDK Ki = 114 mM GAL C6 H12 O6 C([C@@H]1[....
9 1KZB - MAN C6 H12 O6 C([C@@H]1[....
10 1RDJ Ki = 21.7 mM MFB C7 H14 O5 C[C@H]1[C@....
11 1RDM Ki = 5.7 mM MMA C7 H14 O6 CO[C@@H]1[....
70% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 355 families.
1 2MSB Ki = 1.3 mM NAG BMA MAN MAN MAN MAN MAN n/a n/a
2 1KWY - MAN MAN n/a n/a
3 1FIH - NGA C8 H15 N O6 CC(=O)N[C@....
4 4KMB - G4S MAG FUC n/a n/a
5 1BCH - NGA C8 H15 N O6 CC(=O)N[C@....
6 1KWV - NAG C8 H15 N O6 CC(=O)N[C@....
7 1KWU - MMA C7 H14 O6 CO[C@@H]1[....
8 1KWZ - MAN MAN n/a n/a
9 1AFA - MBG C7 H14 O6 CO[C@H]1[C....
10 3KMB - FUC C6 H12 O5 C[C@H]1[C@....
11 2KMB - SIA GAL MAG FUC n/a n/a
12 1KZD - NAG C8 H15 N O6 CC(=O)N[C@....
13 1RDI Ki = 8.8 mM MFU C7 H14 O5 C[C@H]1[C@....
14 1RDL Ki = 5.7 mM MMA C7 H14 O6 CO[C@@H]1[....
15 1KZC - MAN C6 H12 O6 C([C@@H]1[....
16 1KZA - MAN C6 H12 O6 C([C@@H]1[....
17 1KZE - MAN C6 H12 O6 C([C@@H]1[....
18 1RDN Ki = 14.4 mM NDG C8 H15 N O6 CC(=O)N[C@....
19 1RDK Ki = 114 mM GAL C6 H12 O6 C([C@@H]1[....
20 1KZB - MAN C6 H12 O6 C([C@@H]1[....
21 1RDJ Ki = 21.7 mM MFB C7 H14 O5 C[C@H]1[C@....
22 1RDM Ki = 5.7 mM MMA C7 H14 O6 CO[C@@H]1[....
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: MMA; Similar ligands found: 156
No: Ligand ECFP6 Tc MDL keys Tc
1 MBG 1 1
2 AMG 1 1
3 MMA 1 1
4 GYP 1 1
5 MAN MMA 0.651163 0.914286
6 GAL MBG 0.613636 0.914286
7 DR5 0.613636 0.914286
8 M13 0.613636 0.914286
9 MMA MAN 0.613636 0.914286
10 MDM 0.613636 0.914286
11 TRE 0.583333 0.857143
12 GLA MBG 0.581395 0.914286
13 MA3 0.525 0.914286
14 XGP 0.512195 0.674419
15 M1P 0.512195 0.674419
16 G1P 0.512195 0.674419
17 GL1 0.512195 0.674419
18 DEG 0.488889 0.837838
19 BGC BGC 0.478261 0.857143
20 MAN MAN 0.478261 0.857143
21 2M4 0.478261 0.857143
22 WZ1 0.470588 0.842105
23 MAG 0.468085 0.727273
24 2F8 0.468085 0.727273
25 RGG 0.466667 0.909091
26 MAN MMA MAN 0.464286 0.914286
27 GLC SSG SGC SGC MA3 0.462963 0.842105
28 BGC SGC SGC GTM 0.462963 0.842105
29 BGC SSG SSG SGC MA3 0.462963 0.842105
30 GAL MGC 0.462963 0.680851
31 GAT 0.458333 0.674419
32 JZR 0.458333 0.775
33 BHG 0.458333 0.775
34 HEX GLC 0.458333 0.775
35 GLC HEX 0.458333 0.775
36 SMD 0.45098 0.842105
37 2GS 0.45 1
38 KGM 0.44898 0.756098
39 B7G 0.44898 0.756098
40 LAT GLA 0.446809 0.857143
41 2M8 0.446809 0.882353
42 GTM BGC BGC 0.442623 0.842105
43 BOG 0.44 0.756098
44 GLC GLO 0.44 0.909091
45 HSJ 0.44 0.756098
46 BNG 0.44 0.756098
47 R1P 0.439024 0.6
48 GLA GAL 0.4375 0.857143
49 BGC GAL 0.4375 0.857143
50 GLC BGC 0.4375 0.857143
51 GLC GAL 0.4375 0.857143
52 BGC BMA 0.4375 0.857143
53 BMA BMA 0.4375 0.857143
54 EBQ 0.4375 0.810811
55 M3M 0.4375 0.857143
56 LB2 0.4375 0.857143
57 MAB 0.4375 0.857143
58 56N 0.4375 0.805556
59 EBG 0.4375 0.810811
60 CBK 0.4375 0.857143
61 LAT 0.4375 0.857143
62 GAL BGC 0.4375 0.857143
63 BMA GAL 0.4375 0.857143
64 MAL MAL 0.4375 0.833333
65 B2G 0.4375 0.857143
66 MAN GLC 0.4375 0.857143
67 N9S 0.4375 0.857143
68 GAL GLC 0.4375 0.857143
69 GLA GLA 0.4375 0.857143
70 LBT 0.4375 0.857143
71 CBI 0.4375 0.857143
72 BGC GLC 0.4375 0.857143
73 MAL 0.4375 0.857143
74 GAL FUC 0.431373 0.857143
75 BMA BMA MAN 0.431373 0.833333
76 A2G MBG 0.431034 0.680851
77 MBG A2G 0.431034 0.680851
78 GLA GLC 0.428571 0.857143
79 GLA BMA 0.428571 0.857143
80 MLB 0.428571 0.857143
81 MAN BMA 0.428571 0.857143
82 BMA GLA 0.428571 0.857143
83 GAL GAL 0.428571 0.857143
84 LAK 0.428571 0.857143
85 BGC GLA 0.428571 0.857143
86 GLA BGC 0.428571 0.857143
87 WZ2 0.42623 0.842105
88 GLA EGA 0.423077 0.861111
89 GAL PHB 0.423077 0.783784
90 RZM 0.42 0.666667
91 T6P 0.42 0.666667
92 MGL SGC GLC GLC 0.415385 0.842105
93 BGC BGC SGC MGL 0.415385 0.842105
94 VAM 0.415094 0.842105
95 MAN MAN BMA 0.415094 0.857143
96 NAG MBG 0.413793 0.680851
97 HNV 0.413793 0.842105
98 WZ3 0.412698 0.888889
99 MAN MAN MAN 0.411765 0.857143
100 SUC 0.411765 0.789474
101 SER MAN 0.411765 0.75
102 SWE 0.411765 0.789474
103 BMA MAN 0.411765 0.833333
104 DOM 0.411765 0.810811
105 GLC GLC GLC 0.411765 0.857143
106 MAN 7D1 0.411765 0.810811
107 GLC GLC GLC GLC GLC BGC 0.411765 0.857143
108 GLC GLC GLC GLC BGC 0.411765 0.857143
109 GLC FRU 0.411765 0.789474
110 MFU 0.410256 0.727273
111 MFB 0.410256 0.727273
112 XLM 0.407407 0.888889
113 3X8 0.407407 0.763158
114 FK9 0.407407 0.756098
115 GLC GAL GAL 0.403846 0.857143
116 BMA BMA BMA 0.403846 0.857143
117 BGC GLC GLC 0.403846 0.857143
118 MAN BMA BMA BMA BMA 0.403846 0.857143
119 GLC BGC BGC BGC BGC BGC 0.403846 0.857143
120 DXI 0.403846 0.857143
121 CTT 0.403846 0.857143
122 CTR 0.403846 0.857143
123 BGC GLC GLC GLC GLC 0.403846 0.857143
124 MAN MAN BMA BMA BMA BMA 0.403846 0.857143
125 GLC GLC GLC GLC GLC 0.403846 0.857143
126 BGC BGC BGC BGC BGC BGC 0.403846 0.857143
127 CE6 0.403846 0.857143
128 GLA GAL GLC 0.403846 0.857143
129 CE5 0.403846 0.857143
130 BGC BGC BGC GLC 0.403846 0.857143
131 BGC GLC GLC GLC 0.403846 0.857143
132 CE8 0.403846 0.857143
133 MAN BMA BMA 0.403846 0.857143
134 GLC BGC GLC 0.403846 0.857143
135 CT3 0.403846 0.857143
136 GLC GLC BGC GLC GLC GLC GLC 0.403846 0.857143
137 BMA BMA BMA BMA BMA 0.403846 0.857143
138 CEX 0.403846 0.857143
139 B4G 0.403846 0.857143
140 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.403846 0.857143
141 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.403846 0.857143
142 U63 0.403846 0.769231
143 MLR 0.403846 0.857143
144 CEY 0.403846 0.857143
145 GLC BGC BGC 0.403846 0.857143
146 GLC GLC GLC GLC GLC GLC GLC GLC 0.403846 0.857143
147 MT7 0.403846 0.857143
148 GLC GLC GLC GLC GLC GLC GLC 0.403846 0.857143
149 GLC BGC BGC BGC BGC 0.403846 0.857143
150 BMA BMA BMA BMA BMA BMA 0.403846 0.857143
151 MTT 0.403846 0.857143
152 BMA MAN BMA 0.403846 0.857143
153 GLC GLC BGC 0.403846 0.857143
154 BGC GLC GLC GLC GLC GLC GLC 0.403846 0.857143
155 GAL GAL GAL 0.403846 0.857143
156 GLC 7LQ 0.4 0.857143
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1RDL; Ligand: MMA; Similar sites found: 36
This union binding pocket(no: 1) in the query (biounit: 1rdl.bio1) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5N87 N66 0.01981 0.42467 None
2 4D2S DYK 0.008306 0.41065 None
3 5THQ NDP 0.02317 0.40994 None
4 4YHB FAD 0.02042 0.40846 None
5 1TMM APC 0.002615 0.45406 2.65487
6 1TMM HHR 0.002477 0.45406 2.65487
7 3R96 ACO 0.008255 0.4517 2.65487
8 5F5N NAD 0.005951 0.41692 2.65487
9 5W8V 9YP 0.016 0.40647 2.65487
10 5W4W 9WG 0.04021 0.40284 2.65487
11 2RCU BUJ 0.0422 0.40407 3.53982
12 1BB6 UMG 0.002146 0.4313 4.42478
13 1LSZ NDG NAG NAG NAG 0.002561 0.41284 4.42478
14 5N0F 7K2 0.02458 0.40201 4.42478
15 5L83 ASP TRP GLU ILE VAL 0.01301 0.40262 4.46429
16 1NLU IVA PHI TYB 0.002097 0.46003 6.19469
17 1FIW PBZ 0.002979 0.45894 6.19469
18 3UW4 MAA CHG PRO 0DQ 0.01541 0.40181 6.52174
19 5TCI 79V 0.003695 0.45599 7.9646
20 5XDT MB3 0.01165 0.42457 9.73451
21 2PKA BEN 0.002393 0.45553 10.6195
22 4XSU GLC 0.01327 0.43428 10.6195
23 4XSU UDP 0.01327 0.43428 10.6195
24 1G42 CP2 0.01968 0.40201 10.6195
25 3HCN CHD 0.008275 0.42166 12.3894
26 4M0R 644 0.007574 0.44353 13.2743
27 5TZ9 7SD 0.01328 0.42806 26.5487
28 5LXC 7AA 0.02151 0.4103 28.3186
29 3UTU 1TS 0.005219 0.47111 34.5133
30 1TMT DPN PRO ARG 0.004427 0.4588 34.5133
31 2CN0 F25 0.008728 0.43349 34.5133
32 1SL3 170 0.01079 0.43164 34.5133
33 5JQ1 ZPF 0.00000005419 0.71385 35.3982
34 5KTI TRE 6X6 0.0000000006134 0.80228 41.5929
35 2VUZ NAG BMA NAG MAN MAN NAG NAG 0.000000002736 0.60257 41.5929
36 1G1T SIA GAL MAG FUC 0.00007271 0.46146 44.2478
Pocket No.: 2; Query (leader) PDB : 1RDL; Ligand: MMA; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 1rdl.bio1) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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