Receptor
PDB id Resolution Class Description Source Keywords
3TKL 2.18 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE GTP-BOUND RAB1A IN COMPLEX WITH THE COIL DOMAIN OF LIDA FROM LEGIONELLA PNEUMOPHILA HOMO SAPIENS VESICLE TRAFFICKING PROTEIN TRANSPORT-PROTEIN BINDING COMPL
Ref.: STRUCTURAL INSIGHTS INTO A UNIQUE LEGIONELLA PNEUMO EFFECTOR LIDA RECOGNIZING BOTH GDP AND GTP BOUND RA THEIR ACTIVE STATE PLOS PATHOG. V. 8 02528 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GTP A:301;
Valid;
none;
submit data
523.18 C10 H16 N5 O14 P3 c1nc2...
MG A:300;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3TKL 2.18 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE GTP-BOUND RAB1A IN COMPLEX WITH THE COIL DOMAIN OF LIDA FROM LEGIONELLA PNEUMOPHILA HOMO SAPIENS VESICLE TRAFFICKING PROTEIN TRANSPORT-PROTEIN BINDING COMPL
Ref.: STRUCTURAL INSIGHTS INTO A UNIQUE LEGIONELLA PNEUMO EFFECTOR LIDA RECOGNIZING BOTH GDP AND GTP BOUND RA THEIR ACTIVE STATE PLOS PATHOG. V. 8 02528 2012
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 3TKL - GTP C10 H16 N5 O14 P3 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 1205 families.
1 3TKL - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
50% Homology Family (47)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 204 families.
1 3QBT - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
2 5WFO - 5UU C19 H16 Cl F N2 c1cc(ccc1N....
3 6FA3 Kd = 0.038 uM D1Z C30 H36 N4 O5 CN(C)Cc1cc....
4 5WFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
5 5O2T Kd = 3.9 nM GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
6 5WPM - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
7 5WFR - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
8 5UFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
9 6AMB - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
10 6FA1 - D2Z C20 H25 N2 O4 C[NH+](C)C....
11 5UFE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
12 5WFP - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
13 5WHB - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
14 5WPL - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
15 5XCO - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
16 1NVU - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
17 5WHE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
18 3KUC - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
19 1C1Y - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
20 5TAR - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
21 4DXA - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
22 4HDO - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
23 3MJH - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
24 5E95 Kd = 15.7 nM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
25 3CF6 - SP1 C10 H12 N5 O5 P S c1nc(c2c(n....
26 2CJW Kd = 2.5 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
27 6FA4 Kd = 0.051 uM D1W C23 H25 N3 O3 CN(C)Cc1cc....
28 2C5L - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
29 4K81 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
30 1LFD - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
31 4KVG - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
32 3TNF - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
33 1ZC4 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
34 1ZC3 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
35 2A9K - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
36 2A78 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
37 1WQ1 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
38 3TKL - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
39 3DDC - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
40 3KUD - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
41 1TU3 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
42 1UAD Ka = 7260000 M^-1 GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
43 5O74 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
44 3SFV - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
45 4URZ Kd = 3 mM VJP C11 H14 N2 O3 S c1cc(ccc1N....
46 4URX Kd = 1.3 mM HXY C11 H14 Br N c1cc(ccc1C....
47 4URY Kd = 6 mM RV1 C10 H12 N2 O3 S c1cc(ccc1N....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GTP; Similar ligands found: 156
No: Ligand ECFP6 Tc MDL keys Tc
1 GTP 1 1
2 GP3 0.921053 0.973684
3 GDP 0.909091 1
4 GSP 0.853659 0.948718
5 GNH 0.82716 0.986667
6 G1R 0.819277 0.986667
7 GAV 0.811765 0.961039
8 9GM 0.809524 0.973684
9 GNP 0.809524 0.973684
10 GCP 0.797619 0.973684
11 5GP 0.797468 0.986486
12 G 0.797468 0.986486
13 GMV 0.764706 0.973684
14 G2R 0.764045 0.961039
15 G5P 0.755319 0.973684
16 GTG 0.752688 0.936709
17 G2P 0.747126 0.961039
18 G3A 0.744681 0.973684
19 GDD 0.741935 0.961039
20 GDC 0.741935 0.961039
21 GKE 0.741935 0.961039
22 0O2 0.736264 0.986486
23 GP2 0.729412 0.961039
24 6CK 0.726316 0.936709
25 Y9Z 0.723404 0.902439
26 GPG 0.717391 0.961039
27 GFB 0.715789 0.961039
28 GDR 0.715789 0.961039
29 GPD 0.704082 0.925
30 GKD 0.693878 0.961039
31 JB2 0.693878 0.961039
32 GDX 0.686869 0.973684
33 ALF 5GP 0.685393 0.888889
34 GH3 0.681319 0.973333
35 YGP 0.677083 0.901235
36 G3D 0.67033 0.986486
37 GDP AF3 0.659574 0.888889
38 ALF GDP 0.659574 0.888889
39 GDP ALF 0.659574 0.888889
40 DGT 0.659341 0.923077
41 GMP 0.658228 0.88
42 G4P 0.655914 0.986486
43 JB3 0.653846 0.948718
44 NGD 0.647619 0.961039
45 CAG 0.642202 0.880952
46 2MD 0.62963 0.891566
47 MGP 0.619565 0.961039
48 U2G 0.616822 0.936709
49 6G0 0.612903 0.961039
50 MGD 0.612613 0.891566
51 TPG 0.608696 0.840909
52 CG2 0.605505 0.936709
53 GDP 7MG 0.601942 0.911392
54 FEG 0.601852 0.879518
55 G G 0.598039 0.948052
56 ZGP 0.59633 0.869048
57 PGD 0.591304 0.925
58 MD1 0.591304 0.891566
59 3GP 0.590909 0.946667
60 GPX 0.581633 0.946667
61 DGI 0.580645 0.923077
62 IDP 0.576087 0.972973
63 DBG 0.567797 0.948718
64 2GP 0.555556 0.96
65 FE9 0.555556 0.776596
66 G4M 0.547619 0.880952
67 BGO 0.544643 0.924051
68 GCP G 0.543689 0.921053
69 ATP 0.537634 0.92
70 HEJ 0.537634 0.92
71 G1G 0.533898 0.925
72 AQP 0.531915 0.92
73 5FA 0.531915 0.92
74 A G 0.525862 0.935065
75 G A A A 0.525862 0.923077
76 U A G G 0.521368 0.935065
77 HFD 0.520833 0.873418
78 R5I 0.520408 0.946667
79 R7I 0.520408 0.946667
80 01G 0.518868 0.902439
81 P2G 0.510638 0.883117
82 ITT 0.510638 0.868421
83 AKW 0.504348 0.890244
84 GGM 0.504274 0.901235
85 G1R G1R 0.504065 0.924051
86 DGP 0.5 0.910256
87 PGD O 0.5 0.850575
88 MGO 0.5 0.864198
89 DG 0.5 0.910256
90 P1G 0.5 0.871795
91 GTA 0.495495 0.936709
92 PRT 0.490741 0.959459
93 B4P 0.489362 0.894737
94 AP5 0.489362 0.894737
95 IMP 0.489362 0.959459
96 G U 0.487179 0.9
97 7DT 0.484536 0.906667
98 GPC 0.479339 0.879518
99 G C 0.478992 0.9
100 BA3 0.478723 0.894737
101 ADP 0.473684 0.92
102 G2Q 0.471698 0.961039
103 6YZ 0.470588 0.896104
104 G7M 0.46875 0.948052
105 C1Z 0.462963 0.986486
106 25L 0.458716 0.907895
107 A2D 0.457447 0.894737
108 RGT 0.45045 0.909091
109 AGS 0.45 0.873418
110 SAP 0.45 0.873418
111 SGP 0.44898 0.82716
112 A4P 0.445378 0.869048
113 G G G RPC 0.442623 0.875
114 ANP 0.441176 0.896104
115 ACQ 0.441176 0.896104
116 8GT 0.441176 0.875
117 APC G U 0.44 0.886076
118 AT4 0.438776 0.884615
119 G U34 0.438017 0.888889
120 6AD 0.436893 0.841463
121 G G G C 0.433071 0.9125
122 UP5 0.432203 0.873418
123 PCG 0.431373 0.933333
124 C2E 0.431373 0.921053
125 35G 0.431373 0.933333
126 A G C C 0.429688 0.911392
127 T99 0.427184 0.884615
128 5GP 5GP 0.427184 0.883117
129 TAT 0.427184 0.884615
130 AR6 0.425743 0.894737
131 APR 0.425743 0.894737
132 7DD 0.424242 0.906667
133 AN2 0.424242 0.907895
134 DG DG 0.423423 0.865854
135 AD9 0.421569 0.896104
136 M33 0.42 0.883117
137 7D4 0.42 0.835443
138 UCG 0.419847 0.911392
139 HDV 0.419048 0.825
140 H6Y 0.419048 0.946667
141 G C C C 0.416667 0.924051
142 ACP 0.415842 0.896104
143 T5A 0.414634 0.802326
144 A1R 0.412844 0.839506
145 ADQ 0.412844 0.871795
146 MGQ 0.412844 0.935897
147 A3R 0.412844 0.839506
148 MGT 0.411215 0.823529
149 A G U 0.410072 0.888889
150 93A 0.41 0.833333
151 A22 0.407407 0.907895
152 CA0 0.405941 0.896104
153 ATF 0.40566 0.884615
154 AGO 0.404762 0.888889
155 MGV 0.401786 0.890244
156 CGP 0.4 0.86747
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3TKL; Ligand: GTP; Similar sites found with APoc: 71
This union binding pocket(no: 1) in the query (biounit: 3tkl.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 4NCN GTP 3.57143
2 1SKQ GDP 6.12245
3 2BVN GNP 8.16327
4 3WXM GTP 9.18367
5 1GOJ ADP 9.18367
6 2C78 GNP 9.69388
7 5CK5 GDP 10.7143
8 3EC1 GDP 14.7959
9 4DCT GDP 15.7303
10 2VVG ADP 16.4794
11 5FG3 GDP 21.4286
12 1YRB GDP 22.9592
13 4RD0 GDP 23.4694
14 2FH5 GTP 27.551
15 4M9Q GNP 30.6122
16 1KK1 GNP 32.6531
17 1ZJ6 G3D 33.1551
18 1A4R GNH 33.5079
19 1A4R GDP 33.5079
20 2WKQ GTP 33.6735
21 1KSH GDP 34.4086
22 2W2X GSP 34.5946
23 1MH1 GNP 34.9462
24 3SBD GNP 35.2941
25 2FJU GSP 36.5169
26 1HE1 GDP 36.9318
27 1FZQ GDP 38.1215
28 3REF GDP 41.2371
29 1NF3 GNP 41.5385
30 1J2J GTP 41.5663
31 1GWN GTP 41.8367
32 1M7B GTP 41.8478
33 5XC5 GTP 42.6136
34 1GRN GDP 42.9319
35 1E96 GTP 43.2292
36 1I4D GDP 43.75
37 5UPK GNP 43.7838
38 1UPT GTP 43.8596
39 2GCO GNP 43.8776
40 2GCN GDP 43.8776
41 5IRC GDP 45.1613
42 4HAT GNP 45.4082
43 3M1I GTP 45.4082
44 2J0V GDP 45.4082
45 5BXQ GDP 45.4082
46 3CH5 GDP 45.4082
47 1IBR GNP 45.4082
48 1KMQ GNP 45.6522
49 1R4A GNP 46.0606
50 1CXZ GSP 47.2527
51 3Q72 GNP 47.5904
52 5DIF GNP 47.9592
53 5UWQ GNP 47.9592
54 5UWP GNP 47.9592
55 5UWI GNP 47.9592
56 5UWO GNP 47.9592
57 5UWR GNP 47.9592
58 5UWW GNP 47.9592
59 6CIT GNP 47.9592
60 5UWT GNP 47.9592
61 5DHF GNP 47.9592
62 5UWH GNP 47.9592
63 5UWS GNP 47.9592
64 5UWU GNP 47.9592
65 5UWJ GNP 47.9592
66 5DI9 GNP 47.9592
67 1TX4 ALF GDP 48.0226
68 4U5X GNP 48.3146
69 3GJ4 GDP 48.4694
70 3GJ7 GDP 48.4694
71 3GJ5 GDP 48.4694
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