Receptor
PDB id Resolution Class Description Source Keywords
3OKA 2.2 Å EC: 2.4.1.57 CRYSTAL STRUCTURE OF CORYNEBACTERIUM GLUTAMICUM PIMB' IN COM GDP-MAN (TRICLINIC CRYSTAL FORM) CORYNEBACTERIUM GLUTAMICUM GT-B FOLD ALPHA-MANNOSYLTRANSFERASE GDP-MAN BINDING TRANS
Ref.: ACCEPTOR SUBSTRATE DISCRIMINATION IN PHOSPHATIDYL-MYO-INOSITOL MANNOSIDE SYNTHESIS: STRU AND MUTATIONAL ANALYSIS OF MANNOSYLTRANSFERASE CORYNEBACTERIUM GLUTAMICUM PIMB'. J.BIOL.CHEM. V. 285 37741 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDD A:701;
B:701;
 Valid;
Valid;
 none;
none;
 Kd = 19 uM
605.341 C16 H25 N5 O16 P2 c1nc2...
GOL A:801;
 Invalid;
 none;
 submit data
92.094 C3 H8 O3 C(C(C...
SO4 A:601;
A:602;
A:603;
B:601;
B:602;
B:603;
B:604;
C:700;
D:701;
D:702;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3OKA 2.2 Å EC: 2.4.1.57 CRYSTAL STRUCTURE OF CORYNEBACTERIUM GLUTAMICUM PIMB' IN COM GDP-MAN (TRICLINIC CRYSTAL FORM) CORYNEBACTERIUM GLUTAMICUM GT-B FOLD ALPHA-MANNOSYLTRANSFERASE GDP-MAN BINDING TRANS
Ref.: ACCEPTOR SUBSTRATE DISCRIMINATION IN PHOSPHATIDYL-MYO-INOSITOL MANNOSIDE SYNTHESIS: STRU AND MUTATIONAL ANALYSIS OF MANNOSYLTRANSFERASE CORYNEBACTERIUM GLUTAMICUM PIMB'. J.BIOL.CHEM. V. 285 37741 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3OKA Kd = 19 uM GDD C16 H25 N5 O16 P2 c1nc2c(n1[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3OKA Kd = 19 uM GDD C16 H25 N5 O16 P2 c1nc2c(n1[....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3OKA Kd = 19 uM 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 : 3OKA; Ligand: GDD; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3oka.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3OKA; Ligand: GDD; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3oka.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
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