Receptor
PDB id Resolution Class Description Source Keywords
3TNF 2.5 Å NON-ENZYME: OTHER LIDA FROM LEGIONELLA IN COMPLEX WITH ACTIVE RAB8A HOMO SAPIENS PROTEIN TRANSPORT VESICULAR TRAFFICKING GTPASE LEGIONELLAPNEUMOPHILA RAB8A VESICLE RECUITMENT LCV DRRA SIDM RAEFFECTOR VESICULAR TRANSPORT GDP/GTP BINDING RAB-BINDINGGOLGI PLASMAMEMBRANE
Ref.: PROTEIN LIDA FROM LEGIONELLA IS A RAB GTPASE SUPERE PROC.NATL.ACAD.SCI.USA V. 108 17945 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GNP A:200;
Valid;
none;
submit data
522.196 C10 H17 N6 O13 P3 c1nc2...
MG A:199;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
MPD A:1;
A:177;
B:2;
B:3;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
118.174 C6 H14 O2 C[C@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3TNF 2.5 Å NON-ENZYME: OTHER LIDA FROM LEGIONELLA IN COMPLEX WITH ACTIVE RAB8A HOMO SAPIENS PROTEIN TRANSPORT VESICULAR TRAFFICKING GTPASE LEGIONELLAPNEUMOPHILA RAB8A VESICLE RECUITMENT LCV DRRA SIDM RAEFFECTOR VESICULAR TRANSPORT GDP/GTP BINDING RAB-BINDINGGOLGI PLASMAMEMBRANE
Ref.: PROTEIN LIDA FROM LEGIONELLA IS A RAB GTPASE SUPERE PROC.NATL.ACAD.SCI.USA V. 108 17945 2011
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1579 families.
1 3TNF - GNP C10 H17 N6 O13 P3 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 1312 families.
1 3TNF - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
2 3SFV - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (23)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 218 families.
1 5WFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
2 6FA4 Kd = 0.051 uM D1W C23 H25 N3 O3 CN(C)Cc1cc....
3 5O2T Kd = 3.9 nM GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
4 6H46 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 5UFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
6 3KUC - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
7 5TAR - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
8 5E95 Kd = 15.7 nM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 2C5L - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
10 6OB3 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
11 6FA3 Kd = 0.038 uM D1Z C30 H36 N4 O5 CN(C)Cc1cc....
12 6AMB - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
13 4K81 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
14 1LFD - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
15 4KVG - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
16 3TNF - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
17 1ZC4 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
18 2A9K - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
19 2A78 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
20 1WQ1 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
21 3TKL - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
22 3DDC - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
23 3SFV - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GNP; Similar ligands found: 137
No: Ligand ECFP6 Tc MDL keys Tc
1 9GM 1 1
2 GNP 1 1
3 GDP 0.839506 0.973684
4 GP3 0.82716 0.948718
5 GTP 0.809524 0.973684
6 GNH 0.807229 0.986842
7 GCP 0.77907 0.948718
8 G1R 0.77907 0.961039
9 GSP 0.770115 0.925
10 5GP 0.756098 0.960526
11 G 0.756098 0.960526
12 G2R 0.747253 0.936709
13 GMV 0.747126 0.948718
14 GAV 0.714286 0.936709
15 GP2 0.712644 0.936709
16 G2P 0.711111 0.936709
17 Y9Z 0.708333 0.880952
18 GDD 0.690722 0.936709
19 GKE 0.690722 0.936709
20 GDC 0.690722 0.936709
21 G5P 0.686869 0.948718
22 GPG 0.684211 0.936709
23 GFB 0.683673 0.936709
24 GDR 0.683673 0.936709
25 GTG 0.683673 0.91358
26 JB2 0.68 0.936709
27 GKD 0.68 0.936709
28 6CK 0.676768 0.91358
29 G3A 0.676768 0.948718
30 GDX 0.673267 0.948718
31 ALF 5GP 0.67033 0.86747
32 YGP 0.663265 0.879518
33 GPD 0.656863 0.902439
34 GDP AF3 0.645833 0.86747
35 GDP ALF 0.645833 0.86747
36 ALF GDP 0.645833 0.86747
37 JB3 0.641509 0.925
38 DBG 0.640351 0.974359
39 G3D 0.638298 0.960526
40 G4P 0.625 0.960526
41 GMP 0.621951 0.857143
42 NGD 0.62037 0.936709
43 GGM 0.618182 0.925926
44 0O2 0.616162 0.960526
45 KB7 0.612903 0.807229
46 2MD 0.603604 0.870588
47 CAG 0.60177 0.904762
48 FEG 0.590909 0.858824
49 U2G 0.590909 0.91358
50 GDP 7MG 0.590476 0.888889
51 MGD 0.587719 0.870588
52 G G 0.586538 0.924051
53 ZGP 0.585586 0.848837
54 CG2 0.580357 0.91358
55 KBD 0.568627 0.807229
56 ANP 0.568421 0.922078
57 PGD 0.567797 0.902439
58 MD1 0.567797 0.870588
59 3GP 0.56044 0.922078
60 TPG 0.558333 0.822222
61 GH3 0.55 0.948052
62 KBJ 0.54717 0.77907
63 FE9 0.546219 0.778947
64 GPX 0.539216 0.922078
65 G4M 0.539062 0.860465
66 DGI 0.536082 0.9
67 BGO 0.535088 0.901235
68 IDP 0.53125 0.947368
69 DGT 0.53 0.9
70 2GP 0.526882 0.935065
71 G1R G1R 0.520325 0.901235
72 GCP G 0.518868 0.897436
73 A G 0.516949 0.911392
74 U A G G 0.512605 0.911392
75 AGO 0.504202 0.91358
76 G A A A 0.504202 0.9
77 G1G 0.5 0.902439
78 P2G 0.5 0.860759
79 R7I 0.49505 0.922078
80 R5I 0.49505 0.922078
81 MGP 0.49505 0.936709
82 PGD O 0.492063 0.831461
83 6G0 0.490196 0.936709
84 P1G 0.489796 0.85
85 AKW 0.483051 0.869048
86 DG 0.474227 0.8875
87 DGP 0.474227 0.8875
88 G U 0.466667 0.878049
89 IMP 0.463918 0.934211
90 G2Q 0.462963 0.936709
91 GPC 0.459677 0.858824
92 G C 0.459016 0.878049
93 GTA 0.448276 0.91358
94 G7M 0.444444 0.924051
95 MAP 0.439252 0.898734
96 G G G RPC 0.435484 0.853659
97 ADP 0.434343 0.896104
98 AP5 0.434343 0.871795
99 B4P 0.434343 0.871795
100 A2D 0.43299 0.871795
101 AT4 0.43 0.8625
102 G G G C 0.426357 0.890244
103 AU1 0.425743 0.922078
104 SGP 0.425743 0.807229
105 BA3 0.424242 0.871795
106 C2E 0.423077 0.897436
107 35G 0.423077 0.909091
108 PCG 0.423077 0.909091
109 A G C C 0.423077 0.888889
110 APC G U 0.421875 0.864198
111 HEJ 0.421569 0.896104
112 ATP 0.421569 0.896104
113 5GP 5GP 0.419048 0.860759
114 ACQ 0.419048 0.873418
115 AQP 0.417476 0.896104
116 5FA 0.417476 0.896104
117 01G 0.417391 0.880952
118 AN2 0.415842 0.909091
119 UNP 0.415842 0.810127
120 6AD 0.415094 0.821429
121 M33 0.411765 0.860759
122 ITT 0.411765 0.846154
123 G C C C 0.410448 0.901235
124 JSQ 0.409524 0.851852
125 HFD 0.409524 0.851852
126 G U34 0.408 0.86747
127 ACP 0.407767 0.873418
128 KG4 0.407767 0.873418
129 6YZ 0.407407 0.873418
130 APR 0.403846 0.871795
131 AR6 0.403846 0.871795
132 DG DG 0.403509 0.845238
133 A4P 0.403226 0.848837
134 UCG 0.402985 0.888889
135 AGS 0.4 0.851852
136 SAP 0.4 0.851852
137 AD9 0.4 0.873418
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3TNF; Ligand: GNP; Similar sites found with APoc: 24
This union binding pocket(no: 1) in the query (biounit: 3tnf.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 1FQJ ALF 6.32184
2 4NCN GTP 6.32184
3 4NCN GTP 6.32184
4 1SKQ GDP 6.89655
5 2FH5 GTP 12.1495
6 2AWN ADP 14.9425
7 2AWN ADP 14.9425
8 2AWN ADP 14.9425
9 2AWN ADP 14.9425
10 1E96 GTP 47.1264
11 2WKQ GTP 47.1264
12 1MH1 GNP 47.7011
13 2FJU GSP 47.7011
14 2W2X GSP 48.2759
15 2W2X GSP 48.2759
16 5UPK GNP 48.8506
17 1NF3 GNP 48.8506
18 1NF3 GNP 48.8506
19 1NF3 GNP 48.8506
20 1NF3 GNP 48.8506
21 1GRN GDP 49.4253
22 6SGE GTP 49.4253
23 6SGE GTP 49.4253
24 6HXU GTP 49.4253
25 3M1I GTP 50
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