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: 134
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 GKD 0.745098 1
11 JB2 0.745098 0.974359
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 GPG 0.683168 0.974359
23 G2R 0.673267 0.925
24 GMV 0.670103 0.936709
25 G3A 0.660377 0.961538
26 G5P 0.654206 0.961538
27 GAV 0.643564 0.925
28 Y9Z 0.641509 0.892857
29 G2P 0.64 0.925
30 GP2 0.639175 0.925
31 GTG 0.635514 0.925926
32 GDP MG 0.626263 0.888889
33 GMP 0.625 0.87013
34 GDP BEF 0.62 0.86747
35 ADQ 0.61165 0.910256
36 U2G 0.608696 0.95
37 G4M 0.604651 0.916667
38 ALF 5GP 0.60396 0.857143
39 0O2 0.603774 0.948052
40 GTP MG 0.601942 0.888889
41 BEF GDP 0.601942 0.857143
42 YGP 0.601852 0.891566
43 GCP G 0.596154 0.9
44 G4P 0.596154 0.948052
45 G3D 0.592233 0.948052
46 GDP ALF 0.584906 0.857143
47 GDP AF3 0.584906 0.857143
48 CG2 0.584746 0.95
49 G G 0.583333 0.924051
50 NGD 0.581197 0.949367
51 3GP 0.56701 0.935065
52 2MD 0.566667 0.882353
53 CAG 0.565574 0.872093
54 FEG 0.554622 0.892857
55 MGD 0.552846 0.882353
56 ZGP 0.55 0.860465
57 GDP 7MG 0.53913 0.901235
58 TPG 0.539062 0.833333
59 PGD 0.535433 0.914634
60 MD1 0.535433 0.882353
61 2GP 0.535354 0.948052
62 FE9 0.527559 0.770833
63 DBG 0.527132 0.9375
64 G A A A 0.524194 0.936709
65 U A G G 0.52 0.924051
66 G1R G1R 0.515385 0.9375
67 GH3 0.513761 0.935897
68 I2C FE2 CMO CMO 0.5 0.802198
69 DGT 0.495413 0.888889
70 IDP 0.495238 0.935065
71 GPX 0.491071 0.910256
72 DGI 0.485981 0.888889
73 G1G 0.484615 0.914634
74 BGO 0.48 0.9375
75 GPC 0.469231 0.892857
76 G C 0.46875 0.91358
77 P2G 0.466667 0.897436
78 PGD O 0.466667 0.842697
79 2GW 0.466102 0.792683
80 GUD 0.463636 0.8
81 UFM 0.463636 0.8
82 GDU 0.463636 0.8
83 MGP 0.463636 0.925
84 UPG 0.463636 0.8
85 U G A 0.461538 0.902439
86 C5G 0.460177 0.85
87 JBT 0.45977 0.810526
88 6G0 0.459459 0.925
89 G G U 0.459016 0.924051
90 P1G 0.457944 0.886076
91 GGM 0.457364 0.914634
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 ATP 0.422018 0.884615
108 AP5 0.420561 0.884615
109 B4P 0.420561 0.884615
110 ADP 0.420561 0.884615
111 139 0.419847 0.845238
112 AQP 0.418182 0.884615
113 APR 0.418182 0.884615
114 AR6 0.418182 0.884615
115 5FA 0.418182 0.884615
116 AN2 0.416667 0.873418
117 G7M 0.416667 0.9125
118 G G G C 0.416058 0.902439
119 AD9 0.414414 0.8625
120 UCG 0.414286 0.901235
121 A22 0.413793 0.897436
122 A G C C 0.413043 0.901235
123 SGP 0.412844 0.819277
124 ITT 0.412844 0.835443
125 ACQ 0.40708 0.8625
126 ANP 0.40708 0.8625
127 01G 0.406504 0.892857
128 1GW 0.40625 0.764706
129 DG DG 0.404959 0.879518
130 AFH 0.404762 0.855422
131 A4P 0.40458 0.882353
132 G C C C 0.401408 0.91358
133 ATF 0.4 0.851852
134 M33 0.4 0.85
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3OKA; Ligand: GDD; Similar sites found: 39
This union binding pocket(no: 1) in the query (biounit: 3oka.bio2) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WG0 CHD 0.008651 0.41833 None
2 4USF 6UI 0.01384 0.41173 1.97368
3 4YNU LGC 0.04872 0.40814 2.3622
4 4YNU FAD 0.04286 0.40814 2.3622
5 4F97 GDP 0.00001415 0.53412 2.88714
6 4F97 VDO 0.00005588 0.40329 2.88714
7 1XV5 UDP 0.0004261 0.43993 3.41207
8 4CS9 AMP 0.01067 0.4003 4.2328
9 3NW7 LGV 0.03445 0.41242 4.23453
10 3CV3 UDP 0.00001401 0.48897 5.24934
11 5HCY 60D 0.03124 0.41299 6.0423
12 2P1O NLA 0.02155 0.4102 7.08661
13 1F6D UDP 0.003477 0.42266 7.61155
14 1V47 ADX 0.0181 0.40113 8.88252
15 4X1T UDP 0.001255 0.45095 8.92388
16 1MUU SUC 0.01388 0.41087 12.5984
17 2IV3 UDP 0.0000004538 0.62419 14.6982
18 5LWV UDP 0.003866 0.44524 19.0476
19 4GYW UDP 0.006413 0.43942 19.0476
20 5BNW 12V 0.007806 0.43626 19.0476
21 4N39 UDP 0.002396 0.40922 19.0476
22 4P5Z Q7M 0.03743 0.40428 19.0476
23 5W4W 9WG 0.025 0.40042 19.0476
24 1RZU ADP 0.00007899 0.4993 19.1601
25 2XA2 UPG 0.00003326 0.44808 20.4724
26 4X7R UDP 0.0000002942 0.53648 20.7349
27 4X7R 3YW 0.0000001312 0.48746 20.7349
28 4X7R NTO 0.000001155 0.41571 20.7349
29 4PQG UDP 0.000006586 0.47626 23.8095
30 5GZ9 ANP 0.01669 0.40615 23.8095
31 5UIU 8CG 0.02919 0.40227 23.8095
32 2IW1 U2F 0.000002943 0.45101 24.147
33 4XSU GLC 0.0000003761 0.64139 27.8215
34 4XSU UDP 0.0000003761 0.64139 27.8215
35 3Q3H UDP 0.0006747 0.46794 28.5714
36 2GEK GDP 0.0000003205 0.59393 33.3333
37 3MGB GHP 3MY 3FG GHP GHP OMY 3FG 0.007492 0.4198 33.3333
38 5AX9 4KT 0.007104 0.4171 38.0952
39 5JKG 6LF 0.02453 0.41386 42.8571
Pocket No.: 2; Query (leader) PDB : 3OKA; Ligand: GDD; Similar sites found: 2
This union binding pocket(no: 2) in the query (biounit: 3oka.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5FBN 5WF 0.03612 0.40098 3.32103
2 5AJP UDP 0.0127 0.40298 35.2941
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