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 3 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 3 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 3 families.
1 3OKA Kd = 19 uM GDD C16 H25 N5 O16 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GDD; Similar ligands found: 131
No: Ligand ECFP6 Tc MDL keys Tc
1 GDD 1 1
2 GDC 1 1
3 GKE 1 1
4 GDR 0.804124 0.974359
5 GFB 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 GDP BEF 0.613861 0.9
35 ADQ 0.61165 0.910256
36 U2G 0.608696 0.95
37 GTP MG 0.607843 0.923077
38 G4M 0.604651 0.916667
39 ALF 5GP 0.60396 0.857143
40 0O2 0.603774 0.948052
41 YGP 0.601852 0.891566
42 G4P 0.596154 0.948052
43 G3D 0.592233 0.948052
44 GDP ALF 0.584906 0.857143
45 GDP AF3 0.584906 0.857143
46 CG2 0.584746 0.95
47 NGD 0.581197 0.949367
48 3GP 0.56701 0.935065
49 2MD 0.566667 0.882353
50 CAG 0.565574 0.872093
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 G1R G1R 0.515385 0.9375
63 GH3 0.513761 0.935897
64 KBD 0.504425 0.864198
65 GZ0 0.504132 0.987179
66 I2C FE2 CMO CMO 0.503876 0.802198
67 DGT 0.495413 0.888889
68 QBQ 0.495327 0.948052
69 IDP 0.495238 0.935065
70 GPX 0.491071 0.910256
71 R5I 0.490741 0.935065
72 R7I 0.490741 0.935065
73 KBJ 0.487179 0.833333
74 DGI 0.485981 0.888889
75 G1G 0.484615 0.914634
76 BGO 0.48 0.9375
77 GPC 0.469231 0.892857
78 G C 0.46875 0.91358
79 P2G 0.466667 0.897436
80 PGD O 0.466667 0.842697
81 2GW 0.466102 0.792683
82 MGP 0.463636 0.925
83 GDU 0.463636 0.8
84 UPG 0.463636 0.8
85 UFM 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 HQG 0.455357 0.897436
93 DAU 0.448276 0.724138
94 IMP 0.447619 0.922078
95 GTA 0.447154 0.925926
96 DGP 0.443396 0.876543
97 DG 0.443396 0.876543
98 ADP BMA 0.435897 0.886076
99 APC G U 0.433824 0.876543
100 A2D 0.432692 0.884615
101 CZF 0.432432 0.897436
102 AGS 0.427273 0.841463
103 BA3 0.424528 0.884615
104 G2Q 0.423729 0.925
105 ATP 0.422018 0.884615
106 HEJ 0.422018 0.884615
107 AP5 0.420561 0.884615
108 ADP 0.420561 0.884615
109 B4P 0.420561 0.884615
110 139 0.419847 0.845238
111 M7G A2M G 0.41875 0.802198
112 AR6 0.418182 0.884615
113 5FA 0.418182 0.884615
114 AQP 0.418182 0.884615
115 APR 0.418182 0.884615
116 AT4 0.416667 0.851852
117 AN2 0.416667 0.873418
118 G7M 0.416667 0.9125
119 AD9 0.414414 0.8625
120 UCG 0.414286 0.901235
121 A22 0.413793 0.897436
122 SGP 0.412844 0.819277
123 ITT 0.412844 0.835443
124 ANP 0.40708 0.8625
125 ACQ 0.40708 0.8625
126 01G 0.406504 0.892857
127 1GW 0.40625 0.764706
128 AFH 0.404762 0.855422
129 A4P 0.40458 0.882353
130 M33 0.4 0.85
131 ATF 0.4 0.851852
Similar Ligands (3D)
Ligand no: 1; Ligand: GDD; Similar ligands found: 5
No: Ligand Similarity coefficient
1 TDX 0.9085
2 CXY 0.8841
3 UGA 0.8729
4 UD1 0.8671
5 USQ 0.8530
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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