Receptor
PDB id Resolution Class Description Source Keywords
2VMD 1.9 Å NON-ENZYME: OTHER STRUCTURE OF THE COMPLEX OF DISCOIDIN II FROM DICTYOSTELIUM DISCOIDEUM WITH BETA-METHYL-GALACTOSE DICTYOSTELIUM DISCOIDEUM DDR LECTIN AGGREGATION CELL ADHESION
Ref.: STRUCTURE DETERMINATION OF DISCOIDIN II FROM DICTYO DISCOIDEUM AND CARBOHYDRATE BINDING PROPERTIES OF T LECTIN DOMAIN. PROTEINS V. 73 43 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
1PG A:502;
A:503;
Invalid;
Invalid;
none;
none;
submit data
252.305 C11 H24 O6 COCCO...
CA A:500;
Part of Protein;
none;
submit data
40.078 Ca [Ca+2...
CL A:499;
Invalid;
none;
submit data
35.453 Cl [Cl-]
EDO A:504;
Invalid;
none;
submit data
62.068 C2 H6 O2 C(CO)...
MBG A:501;
Valid;
none;
Kd = 0.95 mM
194.182 C7 H14 O6 CO[C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2VMD 1.9 Å NON-ENZYME: OTHER STRUCTURE OF THE COMPLEX OF DISCOIDIN II FROM DICTYOSTELIUM DISCOIDEUM WITH BETA-METHYL-GALACTOSE DICTYOSTELIUM DISCOIDEUM DDR LECTIN AGGREGATION CELL ADHESION
Ref.: STRUCTURE DETERMINATION OF DISCOIDIN II FROM DICTYO DISCOIDEUM AND CARBOHYDRATE BINDING PROPERTIES OF T LECTIN DOMAIN. PROTEINS V. 73 43 2008
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 2VMD Kd = 0.95 mM MBG C7 H14 O6 CO[C@H]1[C....
2 2VMC Kd = 1.15 mM A2G C8 H15 N O6 CC(=O)N[C@....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 2VMD Kd = 0.95 mM MBG C7 H14 O6 CO[C@H]1[C....
2 2VMC Kd = 1.15 mM A2G C8 H15 N O6 CC(=O)N[C@....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 2VMD Kd = 0.95 mM MBG C7 H14 O6 CO[C@H]1[C....
2 2VMC Kd = 1.15 mM A2G C8 H15 N O6 CC(=O)N[C@....
3 2WN3 Kd = 49.4 uM NGA GAL n/a n/a
4 2W95 Kd = 302 uM NGA C8 H15 N O6 CC(=O)N[C@....
5 2WN2 Kd = 27.2 uM A2G GAL n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MBG; 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 : 2VMD; Ligand: MBG; Similar sites found: 170
This union binding pocket(no: 1) in the query (biounit: 2vmd.bio1) has 6 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1NZY BCA 0.004026 0.46424 None
2 1SS4 CIT 0.005022 0.45506 None
3 1SBZ FMN 0.0003919 0.52274 1.52284
4 3IB8 AMP 0.003285 0.4488 1.55642
5 4I71 AGV 0.02424 0.41174 1.55642
6 3F81 STT 0.002316 0.42653 1.63934
7 1V1A KDG 0.00002164 0.56788 1.94553
8 1RY2 AMP 0.0003853 0.51363 1.94553
9 1V1A ADP 0.00105 0.49599 1.94553
10 2DKH FAD 0.009778 0.45048 1.94553
11 2PTZ PAH 0.02122 0.41092 1.94553
12 3MAG 3MA 0.007926 0.41062 1.94553
13 3KJI ADP 0.02667 0.40597 1.9685
14 5FIT AP2 0.004615 0.43919 2.04082
15 3Q3C NAD 0.001622 0.51026 2.33463
16 2AEB ABH 0.002545 0.48197 2.33463
17 4C0C WVH 0.006562 0.47092 2.33463
18 2G36 TRP 0.003084 0.43642 2.33463
19 1FDJ 13P 0.004246 0.42987 2.33463
20 1T8U A3P 0.01386 0.42574 2.33463
21 2HGZ PBF 0.02662 0.41753 2.33463
22 1FDJ 2FP 0.01958 0.40849 2.33463
23 2J0W ADP 0.03158 0.40415 2.33463
24 1EDO NAP 0.02493 0.45337 2.45902
25 4Q3F TLA 0.00009636 0.43321 2.5641
26 1L1Q 9DA 0.003178 0.45795 2.68817
27 2NT8 ATP 0.00006071 0.5603 2.69058
28 2PNZ UDP 0.00003438 0.56751 2.72374
29 1V5F FAD 0.003056 0.53172 2.72374
30 1V5F TPP 0.003056 0.53172 2.72374
31 1JA9 NDP 0.001314 0.52585 2.72374
32 2VJJ RAM GLC GAL NAG NAG GLC 0.001132 0.51667 2.72374
33 1W55 C 0.002024 0.50148 2.72374
34 1JA9 PYQ 0.001095 0.49505 2.72374
35 4HZD COA 0.001687 0.49326 2.72374
36 1W55 GPP 0.001915 0.46029 2.72374
37 3CXO 1N5 0.01203 0.44337 2.72374
38 2PNZ 5GP 0.004469 0.43471 2.72374
39 3CXO 3LR 0.02073 0.42849 2.72374
40 1A5Z OXM 0.0009867 0.42598 2.72374
41 2HGS ADP 0.02187 0.41896 2.72374
42 4HGP KDO 0.007006 0.46043 2.77778
43 4TMK T5A 0.03077 0.46288 2.8169
44 1BTN I3P 0.006154 0.42462 2.83019
45 4U36 TNR 0.009357 0.44093 2.91667
46 3HY3 10F 0.0178 0.42507 2.95567
47 3N5O GSH 0.03244 0.40533 2.97872
48 1BGQ RDC 0.03298 0.41538 3.11111
49 3VHZ L2P GLC MAN SGA 0.0003585 0.55663 3.11284
50 1OMZ UD2 0.0006477 0.52454 3.11284
51 2QIA U20 0.001743 0.50895 3.11284
52 3VHZ SOG 0.004953 0.48936 3.11284
53 1Q3Q ANP 0.008234 0.47423 3.11284
54 4DXJ IPE 0.001532 0.45704 3.11284
55 2QQF A1R 0.005205 0.45554 3.11284
56 1GVF PGH 0.006614 0.42375 3.11284
57 3IB9 BTN 0.001078 0.41465 3.11284
58 1VPO TES 0.02606 0.418 3.19635
59 1SSQ CYS 0.0009479 0.51807 3.50195
60 3O03 GCO 0.0004577 0.49076 3.50195
61 1SAZ ACP 0.02051 0.46146 3.50195
62 3P0K FAD 0.00589 0.448 3.50195
63 2XK9 XK9 0.02753 0.42767 3.50195
64 3O03 NAP 0.02125 0.42536 3.50195
65 2BGM NAJ 0.0001137 0.57761 3.59712
66 2BGM MAX 0.001659 0.47941 3.59712
67 1TRD PGH 0.0151 0.41403 3.6
68 4P3H 25G 0.02065 0.44373 3.62694
69 2FMD MAN MAN 0.0009876 0.48342 3.75
70 1ZFJ IMP 0.0005621 0.52787 3.89105
71 1D09 PAL 0.01918 0.47395 3.89105
72 2NLI LAC 0.01088 0.46305 3.89105
73 2NLI FMN 0.01088 0.46305 3.89105
74 2DUA OXL 0.004127 0.45224 3.89105
75 1TDF FAD 0.02496 0.44081 3.89105
76 2DTX BMA 0.03393 0.42762 3.89105
77 1VBH PEP 0.01281 0.40717 3.89105
78 2PAR TMP 0.04232 0.42535 3.9801
79 1OFH ADP 0.001308 0.48638 4.02299
80 2AZ3 CDP 0.01953 0.40126 4.26829
81 1I9G SAM 0.004486 0.48081 4.28016
82 1RRC ADP 0.00473 0.45284 4.28016
83 1XOC VAL ASP SER LYS ASN THR SER SER TRP 0.0197 0.44136 4.28016
84 3TKA CTN 0.02722 0.40997 4.28016
85 3PNL ADP 0.03611 0.40777 4.28016
86 2H6B 3C4 0.002712 0.49954 4.4
87 4BAS GNP 0.0347 0.40713 4.52261
88 2BNE U5P 0.0002379 0.53628 4.56432
89 3VKX T3 0.0005418 0.49755 4.66926
90 2AMV BIN 0.00281 0.49542 4.66926
91 1OTH PAO 0.001443 0.49302 4.66926
92 1T26 GBD 0.01604 0.47436 4.66926
93 1T26 NAI 0.01604 0.47436 4.66926
94 1Y8O ADP 0.02067 0.40506 4.66926
95 1U7Z PMT 0.02793 0.42627 4.86726
96 1WUR 8DG 0.01631 0.42548 5
97 3NOJ PYR 0.0000762 0.41169 5.04202
98 2V9M CIT 0.0002862 0.4951 5.05837
99 4KCF AKM 0.01933 0.44926 5.05837
100 5T0A A3P 0.004152 0.4402 5.05837
101 4KCF FMN 0.0185 0.41389 5.05837
102 1FP1 SAH 0.02007 0.41213 5.05837
103 1FP1 HCC 0.03806 0.40181 5.05837
104 1UWZ THU 0.01421 0.41959 5.14706
105 4OYA 1VE 0.00007693 0.61141 5.44747
106 2YBQ SAH 0.01211 0.42871 5.44747
107 3H22 B53 0.01104 0.42292 5.44747
108 2WE5 ADP 0.03017 0.40132 5.44747
109 4IS0 1R4 0.00007861 0.54302 5.80913
110 2HCR AMP 0.0005791 0.48172 5.83658
111 3TO7 COA 0.003627 0.47896 5.83658
112 1NW5 SAM 0.007253 0.43992 5.83658
113 3IL6 B83 0.02385 0.41381 5.83658
114 1NME 159 0.001969 0.4597 6.16438
115 2CSN CKI 0.005211 0.45551 6.22568
116 1R37 NAD 0.02878 0.42663 6.22568
117 4G1V FAD 0.02136 0.42654 6.22568
118 4HZX G39 0.0403 0.42353 6.22568
119 1H9G COA MYR 0.002198 0.47636 6.58436
120 4N02 FNR 0.005026 0.48314 6.61479
121 1XHL NDP 0.01252 0.44364 6.61479
122 3CL7 HYN 0.01355 0.43266 6.61479
123 3ZTV ADN 0.01112 0.42277 6.61479
124 3LIH RAF 0.021 0.41488 6.61479
125 4RNX FMN 0.0383 0.40251 6.61479
126 4RNV FMN 0.02567 0.40047 6.61479
127 3H86 AP5 0.001676 0.50459 6.77083
128 4IVG ANP 0.0004551 0.53884 7.00389
129 4TSK NDP 0.001137 0.52206 7.00389
130 1MG1 MAL 0.001845 0.47358 7.00389
131 4TSK TLA 0.005168 0.44733 7.00389
132 1SOW NAD 0.02703 0.42593 7.00389
133 2PWY SAH 0.03101 0.41266 7.00389
134 2FWP CIT 0.004195 0.46739 7.10383
135 2FWP ICR 0.02025 0.43585 7.10383
136 1NVU GTP 0.0005392 0.53838 7.393
137 1XMV ADP 0.000568 0.53448 7.393
138 4NES UDP 0.0127 0.42398 7.393
139 4NES UD1 0.01411 0.42358 7.393
140 3HQJ COA 0.005167 0.44543 7.69231
141 1GSA ADP 0.000118 0.56896 7.7821
142 1GSA GSH 0.0000944 0.56746 7.7821
143 2J8Z NAP 0.02339 0.42574 7.7821
144 1JN2 SFP 0.02027 0.41759 8.01688
145 3S2Y FMN 0.009843 0.43142 8.0402
146 2P4T NAP 0.0002882 0.52827 8.06452
147 2IMP NAI 0.0008728 0.54107 8.17121
148 2IMP LAC 0.000314 0.50839 8.17121
149 3A8U PLP 0.006469 0.44916 8.56031
150 1B66 BIO 0.0004803 0.5032 8.57143
151 1TU3 GNP 0.01976 0.42563 8.86076
152 2YCJ C2F 0.01817 0.41224 8.94942
153 1FIQ FAD 0.03623 0.42126 9.13242
154 2D5X L35 0.01479 0.40421 9.21986
155 2BLE 5GP 0.001925 0.51088 9.33852
156 1CL2 PPG 0.0225 0.4151 9.33852
157 1YAG ATP 0.03321 0.41112 9.33852
158 1C3M MAN MAN 0.000128 0.51788 9.52381
159 2XI7 XI7 0.006905 0.42291 9.72763
160 3UH0 TSB 0.03285 0.41136 9.72763
161 3OZG SSI 0.007425 0.43356 10
162 4GYW UDP 0.01905 0.43399 10.1167
163 3EJ0 11X 0.000006665 0.44892 11.2245
164 3JDW ORN 0.02359 0.40863 12.0623
165 1JGS SAL 0.01407 0.40742 12.3188
166 4UBP HAE 0.001836 0.47089 12.4514
167 1O0D 163 0.004214 0.44784 14.786
168 3DUR KDO 0.0002258 0.40383 16.5289
169 4GQB 0XU 0.003565 0.49138 22.7273
170 2CCV A2G 0.0000005258 0.50446 44.5545
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