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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 28 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 26 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 24 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: 137
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 JB2 0.745098 0.974359
11 GKD 0.745098 1
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 5GP 0.692308 0.948052
20 G 0.692308 0.948052
21 9GM 0.690722 0.936709
22 GNP 0.690722 0.936709
23 GPG 0.683168 0.974359
24 G2R 0.673267 0.925
25 GMV 0.670103 0.936709
26 G3A 0.660377 0.961538
27 G5P 0.654206 0.961538
28 GAV 0.643564 0.925
29 Y9Z 0.641509 0.892857
30 G2P 0.64 0.925
31 GP2 0.639175 0.925
32 GTG 0.635514 0.925926
33 GMP 0.625 0.87013
34 ADQ 0.61165 0.910256
35 U2G 0.608696 0.95
36 G4M 0.604651 0.916667
37 ALF 5GP 0.60396 0.857143
38 0O2 0.603774 0.948052
39 YGP 0.601852 0.891566
40 G4P 0.596154 0.948052
41 G3D 0.592233 0.948052
42 ALF GDP 0.584906 0.857143
43 GDP AF3 0.584906 0.857143
44 GDP ALF 0.584906 0.857143
45 CG2 0.584746 0.95
46 NGD 0.581197 0.949367
47 3GP 0.56701 0.935065
48 2MD 0.566667 0.882353
49 CAG 0.565574 0.872093
50 G G 0.5625 0.936709
51 FEG 0.554622 0.892857
52 MGD 0.552846 0.882353
53 ZGP 0.55 0.860465
54 GDP 7MG 0.53913 0.901235
55 TPG 0.539062 0.833333
56 PGD 0.535433 0.914634
57 MD1 0.535433 0.882353
58 2GP 0.535354 0.948052
59 FE9 0.527559 0.770833
60 DBG 0.527132 0.9375
61 A G 0.524194 0.924051
62 G A A A 0.524194 0.936709
63 U A G G 0.52 0.924051
64 G1R G1R 0.515385 0.9375
65 GH3 0.513761 0.935897
66 GCP G 0.5 0.886076
67 DGT 0.495413 0.888889
68 IDP 0.495238 0.935065
69 GPX 0.491071 0.910256
70 R5I 0.490741 0.935065
71 R7I 0.490741 0.935065
72 G U 0.488 0.91358
73 DGI 0.485981 0.888889
74 G1G 0.484615 0.914634
75 BGO 0.48 0.9375
76 GPC 0.469231 0.892857
77 G C 0.46875 0.91358
78 PGD O 0.466667 0.842697
79 P2G 0.466667 0.897436
80 2GW 0.466102 0.792683
81 GUD 0.463636 0.8
82 UFM 0.463636 0.8
83 MGP 0.463636 0.925
84 UPG 0.463636 0.8
85 GDU 0.463636 0.8
86 C5G 0.460177 0.85
87 JBT 0.45977 0.810526
88 6G0 0.459459 0.925
89 P1G 0.457944 0.886076
90 GGM 0.457364 0.914634
91 AKW 0.456693 0.880952
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 HEJ 0.422018 0.884615
108 ATP 0.422018 0.884615
109 AP5 0.420561 0.884615
110 ADP 0.420561 0.884615
111 B4P 0.420561 0.884615
112 139 0.419847 0.845238
113 AQP 0.418182 0.884615
114 AR6 0.418182 0.884615
115 APR 0.418182 0.884615
116 5FA 0.418182 0.884615
117 AT4 0.416667 0.851852
118 G7M 0.416667 0.9125
119 AN2 0.416667 0.873418
120 G G G C 0.416058 0.902439
121 AD9 0.414414 0.8625
122 UCG 0.414286 0.901235
123 A22 0.413793 0.897436
124 A G C C 0.413043 0.901235
125 SGP 0.412844 0.819277
126 ITT 0.412844 0.835443
127 A G U U 0.410596 0.902439
128 ANP 0.40708 0.8625
129 ACQ 0.40708 0.8625
130 01G 0.406504 0.892857
131 1GW 0.40625 0.764706
132 DG DG 0.404959 0.879518
133 AFH 0.404762 0.855422
134 A4P 0.40458 0.882353
135 G C C C 0.401408 0.91358
136 M33 0.4 0.85
137 ATF 0.4 0.851852
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2I8T; Ligand: GDD; Similar sites found with APoc: 98
This union binding pocket(no: 1) in the query (biounit: 2i8t.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 3KP6 SAL None
2 1KNM LAT None
3 2DTJ THR None
4 3NNT DQA 1.1976
5 1Y7P RIP 1.79641
6 2OUA AES 1.79641
7 1O72 PC 2.39521
8 4QM9 CYS 2.39521
9 1OBD ATP 2.39521
10 1ZGS XMM 2.99401
11 2GEK GDP 2.99401
12 4ZXA H8N 2.99401
13 3SAO NKN 3.125
14 1NFS DED 3.59281
15 5T63 ALA ALA ALA ALA 3.59281
16 5UI2 SUC 3.59281
17 4CNO 9PY 3.59281
18 2WBV SIA 3.59281
19 4HNN LYS 3.59281
20 4B1L FRU 3.63636
21 5AIG VPR 4
22 4A3X LAT 4.19162
23 3OKA GDD 4.19162
24 1C5C TK4 4.19162
25 3OKP GDD 4.19162
26 4CNK MEU 4.19162
27 5ENZ UDP 4.19162
28 3EZ2 ADP 4.19162
29 5WXK TYD 4.19162
30 5NC9 8SZ 4.19162
31 3HRD NIO 4.375
32 4JLS 3ZE 4.60526
33 1FHX 4IP 4.65116
34 6E0D XXX 4.79042
35 5D63 FUC GLA GLA 4.79042
36 2R09 4IP 4.79042
37 1UP7 G6P 4.79042
38 3VSV XYP 4.79042
39 4NS0 PIO 5.26316
40 2ZQO NGA 5.38462
41 2D24 XYS XYS 5.38922
42 4YVN EBS 5.38922
43 4M26 AKG 5.38922
44 2ZUX RAM 5.38922
45 1JIL 485 5.38922
46 1V6A TRE 5.38922
47 2Z49 AMG 5.98802
48 2Z48 NGA 5.98802
49 2Z48 A2G 5.98802
50 2YFO GAL 5.98802
51 2YFO GLA 5.98802
52 2AL2 PEP 5.98802
53 5NM7 GLY 6.01504
54 1F6D UDP 6.58683
55 2HJR CIT 6.58683
56 1JPA ANP 6.58683
57 4P87 4NP 6.58683
58 6FLZ MMA 6.94444
59 5YW5 ADE 7.18563
60 5MST FUM 7.18563
61 2R0D 4IP 7.18563
62 5EOO CIT 7.18563
63 1QVJ RP5 7.78443
64 4LO2 GAL BGC 7.78443
65 4OUJ LBT 7.78443
66 6E1Q CFA 7.78443
67 5FAW CHT 7.78443
68 3Q3H UDP 7.78443
69 4A05 CBI 7.78443
70 3AB4 THR 8.38323
71 5A0U CHT 8.38323
72 1GT4 UNA 8.80503
73 3I7V ATP 8.95522
74 1X9I G6Q 8.98204
75 2FB3 MET 8.98204
76 3VPB GLU 8.98204
77 6EZ6 C5Z 8.98204
78 4UCI ADN 8.98204
79 5YJS SAL 9.58084
80 5J6Y GLC 10.1796
81 5J6Y BGC 10.1796
82 4ZGR NGA GAL 10.1796
83 1JAY F42 10.1796
84 2HZQ STR 11.3772
85 4M3P HCS 12.5749
86 6G7N DAL 12.5749
87 4G9N NGA 13.986
88 5DEQ ARA 16.1677
89 3GZ8 APR 17.284
90 5LPG 71V 17.6829
91 2FVV IHP 17.9641
92 5HZX 2GE 18.5629
93 6EHH 2GE 19.7605
94 5GP0 GPP 20.1342
95 1SWG BTN 22.6562
96 5TQZ GLC 22.6667
97 5ISY NAD 22.7545
98 5GG9 8GT 25.1497
Pocket No.: 2; Query (leader) PDB : 2I8T; Ligand: GDD; Similar sites found with APoc: 64
This union binding pocket(no: 2) in the query (biounit: 2i8t.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 1SL6 GAL NDG FUC None
2 2UVO NDG None
3 2UVO NAG None
4 5LDQ NAP None
5 5IDB BMA None
6 6FA4 D1W None
7 5FPE 3TR 1.79641
8 1Q6O LG6 1.79641
9 2F2T 5IQ 1.86335
10 4YRD 3IT 2.39521
11 4AFH L0B 2.39521
12 4Z7X 3CX 2.39521
13 1BC5 ACE ASN TRP GLU THR PHE 2.99401
14 3OPT AKG 2.99401
15 1W8S FBP 2.99401
16 5EJL C2E 2.99401
17 1NOW IFG 3.59281
18 4TQK NAG 3.59281
19 3H0L ADP 3.59281
20 1MEX RAC 3.59281
21 4JOB TLA 3.59281
22 4ZCW 4NG 3.59281
23 2ET1 GLV 3.59281
24 1KC7 PPR 4.19162
25 4HPP GLU 4.19162
26 5KJW 53C 4.19162
27 2RDE C2E 4.19162
28 5DXT 5H5 4.19162
29 1XL8 OCB 4.19162
30 5A1S FLC 4.19162
31 3CM2 X23 4.61538
32 2W5P CL8 4.69799
33 2VL1 GLY GLY 4.79042
34 5D63 FUC GAL GLA 4.79042
35 2VD9 IN5 4.79042
36 2QX0 PH2 5.03145
37 5Y4R C2E 5.38922
38 5FWJ MMK 5.38922
39 5W75 SUC 5.38922
40 5AE2 FYC 5.38922
41 5AE2 FAD 5.38922
42 1NJJ GET 5.38922
43 1EBG PAH 5.98802
44 5LKC FUC GLA A2G 6.58683
45 4KBA 1QM 6.58683
46 4GLW NMN 7.78443
47 5H9P TD2 7.78443
48 4NZF ARB 7.78443
49 2ICK DMA 8.38323
50 4COV GLA GAL 8.38323
51 4NAE 1GP 8.98204
52 43CA NPO 9.40171
53 4RL4 PPV 9.58084
54 4D52 GXL 9.58084
55 5ZFJ 9BF 10.1796
56 5XLS URA 10.1796
57 3IWD M2T 10.2941
58 3NZ1 3NY 10.7784
59 2CJU PHX 11.5044
60 5FJJ MAN 11.976
61 6CZI 38E 13.3929
62 5YRV 5AD 14.5985
63 2Q89 6CS 15.5689
64 5JQ1 ZPF 15.8621
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