Receptor
PDB id Resolution Class Description Source Keywords
2I8T 1.3 Å EC: 3.6.1.- GDP-MANNOSE MANNOSYL HYDROLASE-CALCIUM-GDP-MANNOSE COMPLEX ESCHERICHIA COLI NUDIX ENZYME LIPOPOLYSACCHARIDE HYDROLASE
Ref.: MOLECULAR BASIS FOR SUBSTRATE SELECTIVITY AND SPECI AN LPS BIOSYNTHETIC ENZYME BIOCHEMISTRY V. 46 4294 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:402;
B:400;
Part of Protein;
Part of Protein;
none;
none;
submit data
40.078 Ca [Ca+2...
GDD A:820;
B:800;
Valid;
Valid;
none;
none;
submit data
605.341 C16 H25 N5 O16 P2 c1nc2...
GOL A:720;
B:700;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2I8T 1.3 Å EC: 3.6.1.- GDP-MANNOSE MANNOSYL HYDROLASE-CALCIUM-GDP-MANNOSE COMPLEX ESCHERICHIA COLI NUDIX ENZYME LIPOPOLYSACCHARIDE HYDROLASE
Ref.: MOLECULAR BASIS FOR SUBSTRATE SELECTIVITY AND SPECI AN LPS BIOSYNTHETIC ENZYME BIOCHEMISTRY V. 46 4294 2007
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 27 families.
1 2I8U - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 2I8T - GDD C16 H25 N5 O16 P2 c1nc2c(n1[....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 25 families.
1 2I8U - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 2I8T - GDD C16 H25 N5 O16 P2 c1nc2c(n1[....
3 1RYA - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 2GT4 - GDD C16 H25 N5 O16 P2 c1nc2c(n1[....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 2I8U - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 2I8T - GDD C16 H25 N5 O16 P2 c1nc2c(n1[....
3 1RYA - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 2GT4 - GDD C16 H25 N5 O16 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GDD; Similar ligands found: 134
No: Ligand ECFP6 Tc MDL keys Tc
1 GDD 1 1
2 GDC 1 1
3 GKE 1 1
4 GFB 0.804124 0.974359
5 GDR 0.804124 0.974359
6 6CK 0.795918 0.95
7 GDX 0.772277 0.987013
8 GP3 0.755556 0.961538
9 GDP 0.747253 0.961039
10 GKD 0.745098 1
11 JB2 0.745098 0.974359
12 GSP 0.744681 0.91358
13 GTP 0.741935 0.961039
14 GNH 0.73913 0.948718
15 G1R 0.734043 0.974026
16 JB3 0.719626 0.962025
17 GPD 0.704762 0.938272
18 GCP 0.697917 0.936709
19 G 0.692308 0.948052
20 5GP 0.692308 0.948052
21 GNP 0.690722 0.936709
22 GPG 0.683168 0.974359
23 G2R 0.673267 0.925
24 GMV 0.670103 0.936709
25 G3A 0.660377 0.961538
26 G5P 0.654206 0.961538
27 GAV 0.643564 0.925
28 Y9Z 0.641509 0.892857
29 G2P 0.64 0.925
30 GP2 0.639175 0.925
31 GTG 0.635514 0.925926
32 GDP MG 0.626263 0.888889
33 GMP 0.625 0.87013
34 GDP BEF 0.62 0.86747
35 ADQ 0.61165 0.910256
36 U2G 0.608696 0.95
37 G4M 0.604651 0.916667
38 ALF 5GP 0.60396 0.857143
39 0O2 0.603774 0.948052
40 GTP MG 0.601942 0.888889
41 BEF GDP 0.601942 0.857143
42 YGP 0.601852 0.891566
43 GCP G 0.596154 0.9
44 G4P 0.596154 0.948052
45 G3D 0.592233 0.948052
46 GDP ALF 0.584906 0.857143
47 GDP AF3 0.584906 0.857143
48 CG2 0.584746 0.95
49 G G 0.583333 0.924051
50 NGD 0.581197 0.949367
51 3GP 0.56701 0.935065
52 2MD 0.566667 0.882353
53 CAG 0.565574 0.872093
54 FEG 0.554622 0.892857
55 MGD 0.552846 0.882353
56 ZGP 0.55 0.860465
57 GDP 7MG 0.53913 0.901235
58 TPG 0.539062 0.833333
59 PGD 0.535433 0.914634
60 MD1 0.535433 0.882353
61 2GP 0.535354 0.948052
62 FE9 0.527559 0.770833
63 DBG 0.527132 0.9375
64 G A A A 0.524194 0.936709
65 U A G G 0.52 0.924051
66 G1R G1R 0.515385 0.9375
67 GH3 0.513761 0.935897
68 I2C FE2 CMO CMO 0.5 0.802198
69 DGT 0.495413 0.888889
70 IDP 0.495238 0.935065
71 GPX 0.491071 0.910256
72 DGI 0.485981 0.888889
73 G1G 0.484615 0.914634
74 BGO 0.48 0.9375
75 GPC 0.469231 0.892857
76 G C 0.46875 0.91358
77 P2G 0.466667 0.897436
78 PGD O 0.466667 0.842697
79 2GW 0.466102 0.792683
80 GUD 0.463636 0.8
81 UFM 0.463636 0.8
82 GDU 0.463636 0.8
83 MGP 0.463636 0.925
84 UPG 0.463636 0.8
85 U G A 0.461538 0.902439
86 C5G 0.460177 0.85
87 JBT 0.45977 0.810526
88 6G0 0.459459 0.925
89 G G U 0.459016 0.924051
90 P1G 0.457944 0.886076
91 GGM 0.457364 0.914634
92 DAU 0.448276 0.724138
93 IMP 0.447619 0.922078
94 GTA 0.447154 0.925926
95 DG 0.443396 0.876543
96 DGP 0.443396 0.876543
97 G U34 0.44186 0.902439
98 ADP BMA 0.435897 0.886076
99 APC G U 0.432836 0.876543
100 A2D 0.432692 0.884615
101 SAP 0.427273 0.841463
102 AGS 0.427273 0.841463
103 A G U 0.424658 0.902439
104 BA3 0.424528 0.884615
105 G G G RPC 0.424242 0.865854
106 G2Q 0.423729 0.925
107 ATP 0.422018 0.884615
108 AP5 0.420561 0.884615
109 B4P 0.420561 0.884615
110 ADP 0.420561 0.884615
111 139 0.419847 0.845238
112 AQP 0.418182 0.884615
113 APR 0.418182 0.884615
114 AR6 0.418182 0.884615
115 5FA 0.418182 0.884615
116 AN2 0.416667 0.873418
117 G7M 0.416667 0.9125
118 G G G C 0.416058 0.902439
119 AD9 0.414414 0.8625
120 UCG 0.414286 0.901235
121 A22 0.413793 0.897436
122 A G C C 0.413043 0.901235
123 SGP 0.412844 0.819277
124 ITT 0.412844 0.835443
125 ACQ 0.40708 0.8625
126 ANP 0.40708 0.8625
127 01G 0.406504 0.892857
128 1GW 0.40625 0.764706
129 DG DG 0.404959 0.879518
130 AFH 0.404762 0.855422
131 A4P 0.40458 0.882353
132 G C C C 0.401408 0.91358
133 ATF 0.4 0.851852
134 M33 0.4 0.85
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2I8T; Ligand: GDD; 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: 2i8t.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2I8T; Ligand: GDD; Similar sites found: 35
This union binding pocket(no: 2) in the query (biounit: 2i8t.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2DTJ THR 0.005676 0.43397 None
2 2UVO NDG 0.03307 0.40932 None
3 4ZBY URA 0.01193 0.42361 1.79641
4 2OUA AES 0.03409 0.40473 1.79641
5 3OPT AKG 0.0351 0.40364 2.99401
6 4ZXA H8N 0.02951 0.40196 2.99401
7 4CNO 9PY 0.02466 0.41012 3.59281
8 4JOB TLA 0.01219 0.40507 3.59281
9 1NFS DED 0.0006067 0.40018 3.59281
10 3OKP GDD 0.01189 0.41017 4.19162
11 1XL8 OCB 0.007786 0.40183 4.19162
12 2VD9 IN5 0.01606 0.40052 4.79042
13 4NS0 PIO 0.008737 0.43196 5.26316
14 2ZQO NGA 0.03879 0.40121 5.38462
15 4M26 AKG 0.02128 0.4148 5.38922
16 5AE2 FYC 0.02239 0.40672 5.38922
17 5AE2 FAD 0.02239 0.40672 5.38922
18 1V6A TRE 0.03301 0.40493 5.38922
19 1EPB REA 0.004835 0.42476 5.4878
20 2Z48 NGA 0.004514 0.45836 5.98802
21 2Z48 A2G 0.01023 0.43662 5.98802
22 4ARU TLA 0.02887 0.40245 5.98802
23 5LKC FUC GLA A2G 0.009594 0.43196 6.58683
24 4KBA 1QM 0.01997 0.4107 6.58683
25 4LO2 GAL BGC 0.00734 0.44244 7.78443
26 3AB4 THR 0.007236 0.43327 8.38323
27 4COV GLA GAL 0.02157 0.41958 8.38323
28 3I7V ATP 0.006429 0.44171 8.95522
29 4NAE 1GP 0.01444 0.42466 8.98204
30 1X9I G6Q 0.02075 0.40215 8.98204
31 5J6Y GLC 0.004152 0.45357 10.1796
32 5J6Y BGC 0.004152 0.45357 10.1796
33 2CJU PHX 0.009084 0.42894 11.5044
34 5FJJ MAN 0.02112 0.41726 11.976
35 3GZ8 APR 0.00004251 0.45868 17.284
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