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Receptor
PDB id Resolution Class Description Source Keywords
3OKP 2 Å EC: 2.4.1.57 CRYSTAL STRUCTURE OF CORYNEBACTERIUM GLUTAMICUM PIMB' BOUND (ORTHORHOMBIC CRYSTAL FORM) CORYNEBACTERIUM GLUTAMICUM GT-B FOLD ALPHA-MANNOSYLTRANSFERASE GDP-MAN TRANSFERASE
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:601;
Valid;
none;
Kd = 19 uM
605.341 C16 H25 N5 O16 P2 c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3OKP 2 Å EC: 2.4.1.57 CRYSTAL STRUCTURE OF CORYNEBACTERIUM GLUTAMICUM PIMB' BOUND (ORTHORHOMBIC CRYSTAL FORM) CORYNEBACTERIUM GLUTAMICUM GT-B FOLD ALPHA-MANNOSYLTRANSFERASE GDP-MAN TRANSFERASE
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 (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3OKC Kd = 36.5 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 3OKP Kd = 19 uM GDD C16 H25 N5 O16 P2 c1nc2c(n1[....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3OKC Kd = 36.5 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 3OKP Kd = 19 uM GDD C16 H25 N5 O16 P2 c1nc2c(n1[....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3OKC Kd = 36.5 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 3OKP 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 : 3OKP; Ligand: GDD; Similar sites found with APoc: 96
This union binding pocket(no: 1) in the query (biounit: 3okp.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 1XVV CCQ 1.01523
3 6H3O FAD 1.52284
4 4ANP 3QI 1.54321
5 3VHE 42Q 1.94986
6 4CNG SAH 1.96078
7 1XF1 CIT 2.03046
8 3HBN UDP 2.12766
9 4YNU LGC 2.28426
10 4YNU FAD 2.28426
11 5XVR TRH 2.34375
12 3RHZ UDP 2.35988
13 5BVE 4VG 2.49307
14 4CS9 AMP 2.6455
15 3UDG TMP 2.65781
16 4GU5 FAD 2.78293
17 4F97 GDP 3.04569
18 4F97 VDO 3.04569
19 4NES UDP 3.20856
20 1XV5 UDP 3.29949
21 3GDN MXN 3.29949
22 1J39 UPG 3.4188
23 4RIF 3R2 3.43008
24 5L13 6ZE 3.5533
25 3E3U NVC 3.5533
26 4YJK URA 3.57143
27 4ZUL UN1 3.80711
28 4JWH SAH 3.83387
29 4G5H UD7 3.85675
30 4G5H NAP 3.85675
31 4B7X NAP 3.86905
32 1VGV UD1 3.90625
33 3KO0 TFP 3.9604
34 4BUY F37 4.16667
35 2I8T GDD 4.19162
36 3CYI ATP 4.54545
37 3EKK GS2 4.56026
38 5NV8 TRH 4.56853
39 5WS9 AMP 4.63158
40 4NFE BEN 4.64135
41 6EQS BV8 4.72727
42 5XVS UDP 5.01319
43 2BW7 ECS 5.02283
44 2XMY CDK 5.03356
45 2WTX VDO 5.07614
46 2WTX UDP 5.07614
47 3CV3 UDP 5.07614
48 4TWP AXI 5.16605
49 3AIA SAM 5.21327
50 3Q3H UDP 5.32995
51 3HRD MCN 5.32995
52 4A4X JUP 5.37634
53 4JWJ SAH 5.94059
54 5O96 SAM 6.12245
55 2Z49 AMG 6.34518
56 2Z48 NGA 6.34518
57 4UCF GLA 6.85279
58 1UPR 4IP 7.31707
59 1F6D UDP 7.36041
60 6MA3 JAJ 7.86802
61 5BNW 12V 7.86802
62 4N3A UDP 7.86802
63 4GYW UDP 7.86802
64 4XCZ T3Q 8.12183
65 5NWD 9C8 8.16327
66 4X1T UDP 8.62944
67 4NAT 2W5 9.375
68 4NAT ADP 9.375
69 1EM6 NBG 9.39086
70 1QM5 PLP 9.64467
71 4CNE SAH 10.1124
72 3TAY MN0 10.4294
73 3MGB GHP 3MY 3FG GHP GHP OMY 3FG 10.6583
74 6EJI UD2 11.2601
75 1NLM UD1 11.2637
76 4PQG UDP 11.9289
77 1MUU SUC 12.1827
78 1N07 FMN 12.2699
79 5ENZ UDP 13.198
80 2IV3 UDP 14.2132
81 5ODQ FAD 15.2174
82 3BEO UDP 15.9898
83 2JLB UDM 16.2437
84 1RZU ADP 18.5279
85 2QZS ADP 18.7817
86 2QZS GLC 18.7817
87 2QZS 250 18.7817
88 6GNF ADP 19.2893
89 2XA2 UPG 19.797
90 4X7R UDP 20.0508
91 4X7R 3YW 20.0508
92 4X7R NTO 20.0508
93 2IW1 U2F 23.5294
94 4XSU GLC 26.9036
95 4XSU UDP 26.9036
96 2GEK GDP 30.7107
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