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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: 118
This union binding pocket(no: 1) in the query (biounit: 3oka.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 6H3O FAD 1.5748
3 3VHE 42Q 1.94986
4 4USF 6UI 1.97368
5 3HBN UDP 2.12766
6 4AG8 AXI 2.21519
7 3RHZ UDP 2.35988
8 5XVR TRH 2.3622
9 2J07 FAD 2.3622
10 2J07 HDF 2.3622
11 4YNU LGC 2.3622
12 4YNU FAD 2.3622
13 2QV6 GTP 2.3622
14 5BVE 4VG 2.49307
15 6CQF F97 2.6936
16 4F97 GDP 2.88714
17 4F97 VDO 2.88714
18 2OFV 242 2.88809
19 3GDN MXN 3.14961
20 2WOX NDP 3.14961
21 5H2U 1N1 3.37079
22 6CZ3 FLJ 3.40909
23 1XV5 UDP 3.41207
24 1J39 UPG 3.4188
25 2WET FAD 3.67454
26 3SXS PP2 3.73134
27 4GU5 FAD 3.93701
28 3KO0 TFP 3.9604
29 1JNR FAD 4
30 2I8T GDD 4.19162
31 4CS9 AMP 4.2328
32 3NW7 LGV 4.23453
33 6EKZ SNP 4.26829
34 2XK9 XK9 4.34783
35 4I6G FAD 4.46194
36 3EKK GS2 4.56026
37 4NFE BEN 4.64135
38 5XVS UDP 5.01319
39 3PP0 03Q 5.02959
40 2HK5 1BM 5.18518
41 3CV3 UDP 5.24934
42 2FFU UDP 5.51181
43 5HCY 60D 6.0423
44 5O96 SAM 6.12245
45 2Z49 AMG 6.56168
46 2Z48 NGA 6.56168
47 2P1O NLA 7.08661
48 2P1O IHP 7.08661
49 4UCF GLA 7.08661
50 3E3U NVC 7.1066
51 1FL2 FAD 7.41935
52 1F6D UDP 7.61155
53 2WTX VDO 7.80591
54 2WTX UDP 7.80591
55 1V47 ADX 8.88252
56 4X1T UDP 8.92388
57 1SG4 CO8 9.23077
58 4ANP 3QI 9.52381
59 5JWC FAD 9.52381
60 1EM6 NBG 9.71129
61 3TAY MN0 10.4294
62 1QM5 PLP 10.4987
63 3WB0 FEG 10.8434
64 1NLM UD1 11.2637
65 1MUU SUC 12.5984
66 1DJL NAP 13.0435
67 4NES UDP 14.2857
68 4GJ3 0XP 14.2857
69 4AT3 LTI 14.2857
70 2IV3 UDP 14.6982
71 3BEO UDP 16.5354
72 2JLB UDM 16.7979
73 6MA3 JAJ 19.0476
74 3NB0 G6P 19.0476
75 4N3A UDP 19.0476
76 4GYW UDP 19.0476
77 1VGV UD1 19.0476
78 5BNW 12V 19.0476
79 4CNE SAH 19.0476
80 5NV8 TRH 19.0476
81 5USZ SKE 19.0476
82 1CS4 FOK 19.0476
83 1CS4 101 19.0476
84 4P5Z Q7M 19.0476
85 5H5F SAM 19.0476
86 5J6D 6H5 19.0476
87 5W4W 9WG 19.0476
88 1RZU ADP 19.1601
89 2QZS ADP 19.4226
90 2QZS 250 19.4226
91 2QZS GLC 19.4226
92 2XA2 UPG 20.4724
93 4X7R UDP 20.7349
94 4X7R 3YW 20.7349
95 4X7R NTO 20.7349
96 4RJD TFP 21.2121
97 4PQG UDP 23.8095
98 4JWH SAH 23.8095
99 4JWJ SAH 23.8095
100 5ENZ UDP 23.8095
101 1OPK P16 23.8095
102 5WXK TYD 23.8095
103 5GZ9 ANP 23.8095
104 1U59 STU 23.8095
105 5A3B APR 23.8095
106 5UIU 8CG 23.8095
107 2IW1 U2F 24.147
108 4XSU GLC 27.8215
109 4XSU UDP 27.8215
110 3Q3H UDP 28.5714
111 5NWD 9C8 28.5714
112 6EJI UD2 28.5714
113 2GEK GDP 33.3333
114 6GNF ADP 33.3333
115 4CNG SAH 33.3333
116 3MGB GHP 3MY 3FG GHP GHP OMY 3FG 33.3333
117 5AX9 4KT 38.0952
118 5JKG 6LF 42.8571
Pocket No.: 2; Query (leader) PDB : 3OKA; Ligand: GDD; Similar sites found with APoc: 2
This union binding pocket(no: 2) in the query (biounit: 3oka.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 5FBN 5WF 3.32103
2 5AJP UDP 35.2941
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