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: 141
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 G 0.692308 0.948052
20 5GP 0.692308 0.948052
21 GNP 0.690722 0.936709
22 9GM 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 GDP AF3 0.584906 0.857143
43 GDP ALF 0.584906 0.857143
44 ALF GDP 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 KB7 0.538462 0.841463
57 MD1 0.535433 0.882353
58 PGD 0.535433 0.914634
59 2GP 0.535354 0.948052
60 FE9 0.527559 0.770833
61 DBG 0.527132 0.9375
62 A G 0.524194 0.924051
63 G A A A 0.524194 0.936709
64 U A G G 0.52 0.924051
65 G1R G1R 0.515385 0.9375
66 GH3 0.513761 0.935897
67 KBD 0.504425 0.864198
68 GCP G 0.5 0.886076
69 DGT 0.495413 0.888889
70 IDP 0.495238 0.935065
71 GPX 0.491071 0.910256
72 R5I 0.490741 0.935065
73 R7I 0.490741 0.935065
74 G U 0.488 0.91358
75 KBJ 0.487179 0.833333
76 DGI 0.485981 0.888889
77 G1G 0.484615 0.914634
78 BGO 0.48 0.9375
79 GPC 0.469231 0.892857
80 G C 0.46875 0.91358
81 PGD O 0.466667 0.842697
82 P2G 0.466667 0.897436
83 2GW 0.466102 0.792683
84 UPG 0.463636 0.8
85 GUD 0.463636 0.8
86 MGP 0.463636 0.925
87 GDU 0.463636 0.8
88 UFM 0.463636 0.8
89 C5G 0.460177 0.85
90 JBT 0.45977 0.810526
91 6G0 0.459459 0.925
92 P1G 0.457944 0.886076
93 GGM 0.457364 0.914634
94 AKW 0.456693 0.880952
95 HQG 0.455357 0.897436
96 DAU 0.448276 0.724138
97 IMP 0.447619 0.922078
98 GTA 0.447154 0.925926
99 DGP 0.443396 0.876543
100 DG 0.443396 0.876543
101 G U34 0.44186 0.902439
102 ADP BMA 0.435897 0.886076
103 APC G U 0.432836 0.876543
104 A2D 0.432692 0.884615
105 AGS 0.427273 0.841463
106 SAP 0.427273 0.841463
107 A G U 0.424658 0.902439
108 BA3 0.424528 0.884615
109 G G G RPC 0.424242 0.865854
110 G2Q 0.423729 0.925
111 ATP 0.422018 0.884615
112 HEJ 0.422018 0.884615
113 AP5 0.420561 0.884615
114 B4P 0.420561 0.884615
115 ADP 0.420561 0.884615
116 139 0.419847 0.845238
117 AR6 0.418182 0.884615
118 AQP 0.418182 0.884615
119 APR 0.418182 0.884615
120 5FA 0.418182 0.884615
121 AT4 0.416667 0.851852
122 AN2 0.416667 0.873418
123 G7M 0.416667 0.9125
124 G G G C 0.416058 0.902439
125 AD9 0.414414 0.8625
126 UCG 0.414286 0.901235
127 A22 0.413793 0.897436
128 A G C C 0.413043 0.901235
129 ITT 0.412844 0.835443
130 SGP 0.412844 0.819277
131 A G U U 0.410596 0.902439
132 ANP 0.40708 0.8625
133 ACQ 0.40708 0.8625
134 01G 0.406504 0.892857
135 1GW 0.40625 0.764706
136 DG DG 0.404959 0.879518
137 AFH 0.404762 0.855422
138 A4P 0.40458 0.882353
139 G C C C 0.401408 0.91358
140 M33 0.4 0.85
141 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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