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: 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 : 3OKP; Ligand: GDD; Similar sites found: 59
This union binding pocket(no: 1) in the query (biounit: 3okp.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1XVV CCQ 0.02582 0.40856 1.01523
2 4ANP 3QI 0.01447 0.4114 1.54321
3 3VHE 42Q 0.01423 0.41049 1.94986
4 4CNG SAH 0.007747 0.42048 1.96078
5 3HBN UDP 0.01012 0.40176 2.12766
6 3RI1 3RH 0.01494 0.40545 2.23642
7 4YNU LGC 0.03825 0.40722 2.28426
8 4YNU FAD 0.03335 0.40722 2.28426
9 3RHZ UDP 0.001893 0.43716 2.35988
10 4GU5 FAD 0.02146 0.4006 2.78293
11 4F97 VDO 0.00008121 0.51468 3.04569
12 4F97 GDP 0.00001069 0.51347 3.04569
13 4NES UDP 0.006396 0.41088 3.20856
14 1XV5 UDP 0.0002525 0.47248 3.29949
15 1J39 UPG 0.000392 0.48383 3.4188
16 4RIF 3R2 0.01736 0.40372 3.43008
17 5L13 6ZE 0.0389 0.40756 3.5533
18 1RYA GDP 0.01593 0.40412 3.75
19 4ZUL UN1 0.02482 0.40001 3.80711
20 4JWH SAH 0.007189 0.41906 3.83387
21 1VGV UD1 0.007274 0.42178 3.90625
22 4BUY F37 0.01801 0.40555 4.16667
23 2I8T GDD 0.01189 0.41017 4.19162
24 3EKK GS2 0.0149 0.4165 4.56026
25 2BW7 ECS 0.04263 0.40405 5.02283
26 2XMY CDK 0.04828 0.4091 5.03356
27 3CV3 UDP 0.000004814 0.55341 5.07614
28 2WTX VDO 0.00002168 0.55093 5.07614
29 2WTX UDP 0.00005515 0.53433 5.07614
30 3AIA SAM 0.006177 0.4095 5.21327
31 3Q3H UDP 0.00103 0.42161 5.32995
32 3HRD MCN 0.01972 0.40943 5.32995
33 4A4X JUP 0.01282 0.40861 5.37634
34 4JWJ SAH 0.008172 0.41487 5.94059
35 1F6D UDP 0.002219 0.41789 7.36041
36 5LWV UDP 0.001959 0.45045 7.86802
37 5BNW 12V 0.002765 0.45004 7.86802
38 4N39 UDP 0.0009612 0.44617 7.86802
39 4GYW UDP 0.003192 0.44575 7.86802
40 4X1T UDP 0.001291 0.44036 8.62944
41 1EM6 NBG 0.005784 0.44394 9.39086
42 1QM5 PLP 0.00112 0.48169 9.64467
43 3TAY MN0 0.01276 0.40725 10.4294
44 1NLM UD1 0.00476 0.41675 11.2637
45 4PQG UDP 0.00000205 0.52028 11.9289
46 1N07 FMN 0.02438 0.4027 12.2699
47 2IV3 UDP 0.00000004783 0.65143 14.2132
48 5ODQ FAD 0.02828 0.40922 15.2174
49 3BEO UDP 0.006479 0.40856 15.9898
50 2JLB UDM 0.009683 0.41442 16.2437
51 1RZU ADP 0.00001391 0.5114 18.5279
52 2XA2 UPG 0.000002738 0.57294 19.797
53 4X7R 3YW 0.00000001619 0.68801 20.0508
54 4X7R NTO 0.0000001094 0.66434 20.0508
55 4X7R UDP 0.00000002126 0.66434 20.0508
56 2IW1 U2F 0.0000004659 0.62126 23.5294
57 4XSU UDP 0.00000005597 0.6625 26.9036
58 4XSU GLC 0.00000005597 0.6625 26.9036
59 2GEK GDP 0.000000445 0.58395 30.7107
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