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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 510 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 (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 391 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 1BCJ Kd = 0.2 mM NGA C8 H15 N O6 CC(=O)N[C@....
8 1KWX - MFB C7 H14 O5 C[C@H]1[C@....
9 1KWU - MMA C7 H14 O6 CO[C@@H]1[....
10 1KWZ - MAN MAN n/a n/a
11 1AFA - MBG C7 H14 O6 CO[C@H]1[C....
12 3KMB - FUC C6 H12 O5 C[C@H]1[C@....
13 2KMB - SIA GAL MAG FUC n/a n/a
14 1KZD - NAG C8 H15 N O6 CC(=O)N[C@....
15 1RDI Ki = 8.8 mM MFU C7 H14 O5 C[C@H]1[C@....
16 1RDL Ki = 5.7 mM MMA C7 H14 O6 CO[C@@H]1[....
17 1KZC - MAN C6 H12 O6 C([C@@H]1[....
18 1KZA - MAN C6 H12 O6 C([C@@H]1[....
19 1KZE - MAN C6 H12 O6 C([C@@H]1[....
20 1RDN Ki = 14.4 mM NDG C8 H15 N O6 CC(=O)N[C@....
21 1RDK Ki = 114 mM GAL C6 H12 O6 C([C@@H]1[....
22 1KZB - MAN C6 H12 O6 C([C@@H]1[....
23 1RDJ Ki = 21.7 mM MFB C7 H14 O5 C[C@H]1[C@....
24 1RDM Ki = 5.7 mM MMA C7 H14 O6 CO[C@@H]1[....
50% Homology Family (47)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 174 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 - G4S MAG FUC 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 - SIA GAL MAG 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 MLR C18 H32 O16 C([C@@H]1[....
35 3G83 - MAN MAN n/a n/a
36 2RID ic50 = 1.7 mM 291 C11 H19 N O8 C=CCO[C@@H....
37 1KZD - NAG C8 H15 N O6 CC(=O)N[C@....
38 1RDI Ki = 8.8 mM MFU C7 H14 O5 C[C@H]1[C@....
39 1RDL Ki = 5.7 mM MMA C7 H14 O6 CO[C@@H]1[....
40 1KZC - MAN C6 H12 O6 C([C@@H]1[....
41 1KZA - MAN C6 H12 O6 C([C@@H]1[....
42 1KZE - MAN C6 H12 O6 C([C@@H]1[....
43 1RDN Ki = 14.4 mM NDG C8 H15 N O6 CC(=O)N[C@....
44 1RDK Ki = 114 mM GAL C6 H12 O6 C([C@@H]1[....
45 1KZB - MAN C6 H12 O6 C([C@@H]1[....
46 1RDJ Ki = 21.7 mM MFB C7 H14 O5 C[C@H]1[C@....
47 1RDM Ki = 5.7 mM MMA C7 H14 O6 CO[C@@H]1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MMA; Similar ligands found: 169
No: Ligand ECFP6 Tc MDL keys Tc
1 MMA 1 1
2 GYP 1 1
3 AMG 1 1
4 MBG 1 1
5 MAN MMA 0.651163 0.914286
6 GAL MBG 0.613636 0.914286
7 M13 0.613636 0.914286
8 DR5 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 G1P 0.512195 0.674419
15 M1P 0.512195 0.674419
16 GL1 0.512195 0.674419
17 XGP 0.512195 0.674419
18 BQZ 0.5 0.878788
19 DEG 0.488889 0.837838
20 2M4 0.478261 0.857143
21 WZ1 0.470588 0.842105
22 MAG 0.468085 0.727273
23 EBQ 0.468085 0.861111
24 2F8 0.468085 0.727273
25 RGG 0.466667 0.909091
26 MAN MMA MAN 0.464286 0.914286
27 BGC SSG SSG SGC MA3 0.462963 0.842105
28 GLC SSG SGC SGC MA3 0.462963 0.842105
29 BGC SGC SGC GTM 0.462963 0.842105
30 GAL MGC 0.462963 0.680851
31 GAT 0.458333 0.674419
32 GLC HEX 0.458333 0.775
33 JZR 0.458333 0.775
34 BHG 0.458333 0.775
35 SMD 0.45098 0.842105
36 2GS 0.45 1
37 B7G 0.44898 0.756098
38 KGM 0.44898 0.756098
39 LAT GLA 0.446809 0.857143
40 2M8 0.446809 0.882353
41 GTM BGC BGC 0.442623 0.842105
42 BNG 0.44 0.756098
43 GLC GLO 0.44 0.909091
44 BOG 0.44 0.756098
45 HSJ 0.44 0.756098
46 R1P 0.439024 0.6
47 GLA GAL 0.4375 0.857143
48 GLC GAL 0.4375 0.857143
49 BGC BMA 0.4375 0.857143
50 LBT 0.4375 0.857143
51 LAT 0.4375 0.857143
52 EBG 0.4375 0.810811
53 MAL 0.4375 0.857143
54 MAN GLC 0.4375 0.857143
55 56N 0.4375 0.805556
56 GLA GLA 0.4375 0.857143
57 LB2 0.4375 0.857143
58 N9S 0.4375 0.857143
59 NGR 0.4375 0.857143
60 CBI 0.4375 0.857143
61 GAL BGC 0.4375 0.857143
62 M3M 0.4375 0.857143
63 MAB 0.4375 0.857143
64 BMA GAL 0.4375 0.857143
65 CBK 0.4375 0.857143
66 BGC GAL 0.4375 0.857143
67 B2G 0.4375 0.857143
68 GAL FUC 0.431373 0.857143
69 MBG A2G 0.431034 0.680851
70 A2G MBG 0.431034 0.680851
71 GLA BGC 0.428571 0.857143
72 GLC GLC 0.428571 0.857143
73 BGC GLA 0.428571 0.857143
74 MAN BMA 0.428571 0.857143
75 BMA MAN 0.428571 0.857143
76 MAN MAN 0.428571 0.857143
77 GLA GLC 0.428571 0.857143
78 BMA GLA 0.428571 0.857143
79 BGC GLC 0.428571 0.857143
80 GLC BGC 0.428571 0.857143
81 LAK 0.428571 0.857143
82 GAL GAL 0.428571 0.857143
83 MLB 0.428571 0.857143
84 GLA BMA 0.428571 0.857143
85 GAL GLC 0.428571 0.857143
86 WZ2 0.42623 0.842105
87 GLA EGA 0.423077 0.861111
88 GAL PHB 0.423077 0.783784
89 T6P 0.42 0.666667
90 RZM 0.42 0.666667
91 BGC BGC SGC MGL 0.415385 0.842105
92 MGL SGC GLC GLC 0.415385 0.842105
93 MGL SGC BGC BGC 0.415385 0.842105
94 BMA IFM 0.415094 0.652174
95 MAN MAN BMA 0.415094 0.857143
96 VAM 0.415094 0.842105
97 IFM BMA 0.415094 0.652174
98 BMA BMA MAN 0.415094 0.857143
99 IFM BGC 0.415094 0.652174
100 NAG MBG 0.413793 0.680851
101 HNV 0.413793 0.842105
102 WZ3 0.412698 0.888889
103 GLC GLC GLC 0.411765 0.857143
104 DOM 0.411765 0.810811
105 SWE 0.411765 0.789474
106 MAN MAN MAN 0.411765 0.857143
107 BGC BGC 0.411765 0.833333
108 BMA BMA 0.411765 0.833333
109 MAN 7D1 0.411765 0.810811
110 GLC GLC GLC GLC GLC BGC 0.411765 0.857143
111 BMA MAN MAN 0.411765 0.857143
112 SUC 0.411765 0.789474
113 GLC GLC GLC GLC BGC 0.411765 0.857143
114 MFB 0.410256 0.727273
115 MFU 0.410256 0.727273
116 XLM 0.407407 0.888889
117 DMJ MAN 0.407407 0.638298
118 NOJ BGC 0.407407 0.638298
119 GLC DMJ 0.407407 0.638298
120 3X8 0.407407 0.763158
121 FK9 0.407407 0.756098
122 GLC BGC BGC BGC BGC BGC 0.403846 0.857143
123 MTT 0.403846 0.857143
124 MT7 0.403846 0.857143
125 GLC BGC BGC BGC BGC 0.403846 0.857143
126 MLR 0.403846 0.857143
127 GLC BGC BGC BGC 0.403846 0.857143
128 BGC BGC BGC GLC 0.403846 0.857143
129 BGC BGC BGC BGC BGC 0.403846 0.857143
130 GLA GAL BGC 0.403846 0.857143
131 SER MAN 0.403846 0.697674
132 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.403846 0.857143
133 CEX 0.403846 0.857143
134 CE6 0.403846 0.857143
135 BGC GLC GLC GLC GLC GLC GLC 0.403846 0.857143
136 BMA BMA BMA 0.403846 0.857143
137 GLC GLC GLC GLC GLC 0.403846 0.857143
138 CTR 0.403846 0.857143
139 BMA MAN BMA 0.403846 0.857143
140 GLC GAL GAL 0.403846 0.857143
141 CE5 0.403846 0.857143
142 U63 0.403846 0.769231
143 BGC BGC BGC 0.403846 0.857143
144 CT3 0.403846 0.857143
145 GLA GAL GLC 0.403846 0.857143
146 DXI 0.403846 0.857143
147 BGC GLC GLC GLC 0.403846 0.857143
148 BGC BGC BGC BGC BGC BGC 0.403846 0.857143
149 GLC BGC GLC 0.403846 0.857143
150 MAN BMA BMA BMA BMA BMA 0.403846 0.857143
151 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.403846 0.857143
152 BGC GLC GLC GLC GLC 0.403846 0.857143
153 BGC BGC BGC BGC 0.403846 0.857143
154 CE8 0.403846 0.857143
155 CEY 0.403846 0.857143
156 MAN BMA BMA BMA BMA 0.403846 0.857143
157 BGC GLC GLC 0.403846 0.857143
158 BGC BGC GLC 0.403846 0.857143
159 BMA BMA BMA BMA BMA BMA 0.403846 0.857143
160 CTT 0.403846 0.857143
161 GLC GLC BGC 0.403846 0.857143
162 MAN MAN BMA BMA BMA BMA 0.403846 0.857143
163 GLC BGC BGC 0.403846 0.857143
164 MAN BMA BMA 0.403846 0.857143
165 B4G 0.403846 0.857143
166 BMA BMA BMA BMA BMA 0.403846 0.857143
167 GAL GAL GAL 0.403846 0.857143
168 GLC 7LQ 0.4 0.857143
169 IFM MAN 0.4 0.652174
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1RDL; Ligand: MMA; Similar sites found with APoc: 160
This union binding pocket(no: 1) in the query (biounit: 1rdl.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 2AIQ BEN None
2 3APT FAD None
3 1PQ7 ARG None
4 6FNU FAD None
5 4QVB F42 None
6 5N87 N66 None
7 4UUU SAM None
8 3E3U NVC None
9 3R5W F42 None
10 5THQ NDP None
11 4KOT CE3 None
12 4YHB FAD None
13 4G6I RS3 None
14 5TP0 BRN 0.884956
15 5YAK FMN 1.76991
16 2Z6C FMN 1.76991
17 2QX0 APC 2.65487
18 1TMM HHR 2.65487
19 1TMM APC 2.65487
20 1YF4 CYS TYR PHE GLN ASN CYS PRO ARG GLY NH2 2.65487
21 3R96 AMP 2.65487
22 3R96 ACO 2.65487
23 6B74 BEN 2.65487
24 4KBA 1QM 2.65487
25 5F5N NAD 2.65487
26 1H5Q NAP 2.65487
27 5W4W 9WG 2.65487
28 1XUJ BOZ 3.53982
29 1ETS MID 3.53982
30 5HI5 63Q 3.53982
31 5EGM 5NY 3.53982
32 2CWH NDP 3.53982
33 1P4A PCP 3.53982
34 1O98 2PG 3.53982
35 1TKK ALA GLU 3.53982
36 1KZL CRM 3.53982
37 2RCU BUJ 3.53982
38 2P8O BVA 4.12371
39 1A0J BEN 4.42478
40 1BB6 UMG 4.42478
41 4DP3 MMV 4.42478
42 2VBQ BSJ 4.42478
43 4MAF ADX 4.42478
44 1LSZ NDG NAG NAG NAG 4.42478
45 4P86 5GP 4.42478
46 3RHZ UDP 4.42478
47 5N0F 7K2 4.42478
48 5K9B FMN 4.42478
49 5CMK GLU 4.42478
50 5U97 PIT 4.42478
51 5L83 ASP TRP GLU ILE VAL 4.46429
52 1UTJ ABN 5.30973
53 5Q0F 9FA 5.30973
54 4MTI 2DX 5.30973
55 4D8N 0HM 5.30973
56 5M6N 7H9 5.30973
57 6A1G 9OL 5.30973
58 3WDM ADN 5.30973
59 1DQN IMU 5.30973
60 2JFQ DGL 5.30973
61 5OYH T99 5.30973
62 3N9R TD3 5.30973
63 4MN3 ACE PHE ALA TYR M3L SER NH2 5.35714
64 1NLU IVA PHI TYB 6.19469
65 4O97 NTX 6.19469
66 1FIW PBZ 6.19469
67 5ETR APC 6.19469
68 5ETR 5RW 6.19469
69 1OSS BEN 6.19469
70 3R5Z F42 6.19469
71 1DAK DPU 6.19469
72 1DAK ADP 6.19469
73 4JWH SAH 6.19469
74 5GWT NAD 6.19469
75 3KF3 FRU 6.19469
76 4JAW GAL NGT 6.19469
77 3UW4 MAA CHG PRO 0DQ 6.52174
78 1RIW OSC 6.66667
79 1BHX R56 6.66667
80 1RTF BEN 7.07965
81 2ZA5 2FF 7.07965
82 1KRH FAD 7.07965
83 5JCA FAD 7.07965
84 1UPF URF 7.07965
85 4YRY FAD 7.07965
86 6APV 3L4 7.07965
87 4NBU NAI 7.07965
88 3N0S ACO 7.07965
89 1O5E 132 7.9646
90 5FFF NAP 7.9646
91 5FAH 5VT 7.9646
92 5TCI 79V 7.9646
93 1PZM 5GP 7.9646
94 3QWI CUE 7.9646
95 3QWI NAP 7.9646
96 2AHR NAP 7.9646
97 3UR0 SVR 8.84956
98 1OJZ NAD 8.84956
99 4OM8 NAD 8.84956
100 6FCX FAD 9.73451
101 4NFE BEN 9.73451
102 5XDT MB3 9.73451
103 1YBH CIE 9.73451
104 3N75 G4P 9.73451
105 4JWJ SAH 9.73451
106 2PKA BEN 10.6195
107 4XSU GLC 10.6195
108 4XSU UDP 10.6195
109 6EGU 43Y 10.6195
110 6AR9 3L4 10.6195
111 1G42 CP2 10.6195
112 2EC9 24X 10.6667
113 2VH6 GSV 11.5044
114 2H9E DTY ILE ARG LEU LPD 11.5044
115 1NFU RRP 11.5044
116 1T0I FMN 11.5044
117 3HCN CHD 12.3894
118 6FYV 3NG 12.3894
119 4UAI 3GG 13.2353
120 4M0R 644 13.2743
121 3IGZ 3PG 13.2743
122 3IGZ 2PG 13.2743
123 3R5Y F42 13.2743
124 2OQ5 BEN 14.1593
125 6AIX A3P 14.1593
126 3E8T UQ8 14.1593
127 3HDY GDU 14.1593
128 3HDY FAD 14.1593
129 2A5F NAD 15.0442
130 6DA9 FMN 15.0442
131 2J83 BAT 15.9292
132 5NB7 8NQ 16.8142
133 4M52 FAD 17.6991
134 1LZR NAG NAG NAG NAG 18.5841
135 1FP1 SAH 18.5841
136 2BDG PBZ 19.469
137 4JWF SAH 19.469
138 1VD3 U2P 19.469
139 3MBI HSX 20.354
140 2HXW FLC 20.354
141 4AU8 Z3R 23.0089
142 2P3T 993 23.0769
143 5W7C DAO FTT 24.7788
144 5ZTN CUR 30.0885
145 2ANM CDO 34.5133
146 2ANK N12 34.5133
147 2FEQ 34P 34.5133
148 1TMT DPN PRO ARG 34.5133
149 2FES 3SP 34.5133
150 1NZQ 162 34.5133
151 1EB1 ZAL PRO MMO 34.5133
152 4AX9 N5N 34.5133
153 1D9I 00P 34.5133
154 2CN0 F25 34.5133
155 1SL3 170 34.5133
156 3VXE DPN PRO ARG 35.2941
157 5JQ1 ZPF 35.3982
158 5KTI TRE 6X6 41.5929
159 1G1T SIA GAL MAG FUC 44.2478
160 5G6U YJM 45.1327
161 1A2C 34H LEU PRJ OAR 50
Pocket No.: 2; Query (leader) PDB : 1RDL; Ligand: MMA; Similar sites found with APoc: 15
This union binding pocket(no: 2) in the query (biounit: 1rdl.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 3SVL FMN None
2 6HT0 GQ8 1.76991
3 2C6Q IMP 5.30973
4 1KYZ SAH 7.07965
5 5KOD AMP 8.84956
6 6GIU L69 8.84956
7 1KUV CA5 8.84956
8 3IR1 MET 9.73451
9 4EO3 FMN 9.73451
10 5HRA DAS 13.2743
11 4N8I COA 15.0442
12 3OZG SSI 16.8142
13 4B1W ATP 18.75
14 5Y86 HRM 22.1239
15 6ASZ GLN THR ALA ARG M3L SER 23.1884
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