Receptor
PDB id Resolution Class Description Source Keywords
5O74 2.5 Å EC: 2.7.7.- CRYSTAL STRUCTURE OF HUMAN RAB1B COVALENTLY BOUND TO THE GEF DRRA/SIDM FROM LEGIONELLA PNEUMOPHILA IN THE PRESENCE OF GD LEGIONELLA PNEUMOPHILA RAB1B DRRA EXCHANGE FACTOR LEGIONELLA PNEUMOPHILA HYDROL
Ref.: PROXIMITY-TRIGGERED COVALENT STABILIZATION OF LOW-A PROTEIN COMPLEXES IN VITRO AND IN VIVO. ANGEW. CHEM. INT. ED. ENGL. V. 56 15737 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP F:500;
L:500;
D:500;
J:500;
H:500;
B:500;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5O74 2.5 Å EC: 2.7.7.- CRYSTAL STRUCTURE OF HUMAN RAB1B COVALENTLY BOUND TO THE GEF DRRA/SIDM FROM LEGIONELLA PNEUMOPHILA IN THE PRESENCE OF GD LEGIONELLA PNEUMOPHILA RAB1B DRRA EXCHANGE FACTOR LEGIONELLA PNEUMOPHILA HYDROL
Ref.: PROXIMITY-TRIGGERED COVALENT STABILIZATION OF LOW-A PROTEIN COMPLEXES IN VITRO AND IN VIVO. ANGEW. CHEM. INT. ED. ENGL. V. 56 15737 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 5O74 - GDP C10 H15 N5 O11 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 20 families.
1 5O74 - GDP C10 H15 N5 O11 P2 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: GDP; Similar ligands found: 161
No: Ligand ECFP6 Tc MDL keys Tc
1 GDP 1 1
2 GTP 0.909091 1
3 GP3 0.881579 0.973684
4 GNH 0.858974 0.986667
5 9GM 0.839506 0.973684
6 GNP 0.839506 0.973684
7 G 0.828947 0.986486
8 5GP 0.828947 0.986486
9 G1R 0.82716 0.986667
10 GCP 0.82716 0.973684
11 GSP 0.817073 0.948718
12 GAV 0.797619 0.961039
13 GMV 0.792683 0.973684
14 G2P 0.77381 0.961039
15 G2R 0.770115 0.961039
16 GP2 0.756098 0.961039
17 GDC 0.747253 0.961039
18 GKE 0.747253 0.961039
19 GDD 0.747253 0.961039
20 GPG 0.741573 0.961039
21 G3D 0.732558 0.986486
22 ALF 5GP 0.729412 0.888889
23 Y9Z 0.728261 0.902439
24 G5P 0.723404 0.973684
25 GFB 0.72043 0.961039
26 GTG 0.72043 0.936709
27 GDR 0.72043 0.961039
28 G4P 0.715909 0.986486
29 G3A 0.712766 0.973684
30 6CK 0.712766 0.936709
31 GDP AF3 0.7 0.888889
32 ALF GDP 0.7 0.888889
33 GDP ALF 0.7 0.888889
34 YGP 0.698925 0.901235
35 GKD 0.697917 0.961039
36 JB2 0.697917 0.961039
37 GDX 0.690722 0.973684
38 GPD 0.690722 0.925
39 GMP 0.684211 0.88
40 0O2 0.666667 0.986486
41 JB3 0.656863 0.948718
42 NGD 0.650485 0.961039
43 DGI 0.636364 0.923077
44 GDP 7MG 0.636364 0.911392
45 U2G 0.634615 0.936709
46 GPX 0.634409 0.946667
47 G G 0.632653 0.948052
48 IDP 0.632184 0.972973
49 2MD 0.632075 0.891566
50 CAG 0.62963 0.880952
51 CG2 0.622642 0.936709
52 FEG 0.619048 0.879518
53 MGD 0.614679 0.891566
54 ZGP 0.613208 0.869048
55 GH3 0.612903 0.973333
56 3GP 0.611765 0.946667
57 MD1 0.607143 0.891566
58 PGD 0.59292 0.925
59 DGT 0.591398 0.923077
60 BGO 0.588785 0.924051
61 TPG 0.582609 0.840909
62 DBG 0.582609 0.948718
63 2GP 0.574713 0.96
64 FE9 0.570175 0.776596
65 GCP G 0.56 0.921053
66 A G 0.553571 0.935065
67 G A A A 0.553571 0.923077
68 MGP 0.553191 0.961039
69 U A G G 0.548673 0.935065
70 G4M 0.548387 0.880952
71 6G0 0.547368 0.961039
72 G1R G1R 0.542373 0.924051
73 P2G 0.527473 0.883117
74 PGD O 0.525 0.850575
75 ADP 0.522222 0.92
76 R5I 0.520833 0.946667
77 R7I 0.520833 0.946667
78 GGM 0.517544 0.901235
79 DGP 0.516484 0.910256
80 DG 0.516484 0.910256
81 P1G 0.516129 0.871795
82 G U 0.513274 0.9
83 G1G 0.508475 0.925
84 IMP 0.505495 0.959459
85 AKW 0.504425 0.890244
86 G C 0.504348 0.9
87 GPC 0.491525 0.879518
88 G7M 0.483871 0.948052
89 6AD 0.479592 0.841463
90 ATP 0.473684 0.92
91 HEJ 0.473684 0.92
92 G2Q 0.471154 0.961039
93 5FA 0.46875 0.92
94 AQP 0.46875 0.92
95 GTA 0.468468 0.936709
96 7DD 0.468085 0.906667
97 G G G RPC 0.466102 0.875
98 SGP 0.463158 0.82716
99 01G 0.462963 0.902439
100 HFD 0.459184 0.873418
101 B4P 0.457447 0.894737
102 AP5 0.457447 0.894737
103 A2D 0.456522 0.894737
104 6YZ 0.455446 0.896104
105 G G G C 0.455285 0.9125
106 5GP 5GP 0.454545 0.883117
107 ANP 0.454545 0.896104
108 ACQ 0.454545 0.896104
109 AT4 0.452632 0.884615
110 A G C C 0.451613 0.911392
111 APC G U 0.45082 0.886076
112 PRT 0.449541 0.959459
113 G U34 0.449153 0.888889
114 DG DG 0.448598 0.865854
115 ITT 0.447917 0.868421
116 BA3 0.446809 0.894737
117 C2E 0.444444 0.921053
118 PCG 0.444444 0.933333
119 35G 0.444444 0.933333
120 MGO 0.441176 0.864198
121 AN2 0.4375 0.907895
122 G C C C 0.4375 0.924051
123 M33 0.43299 0.883117
124 UCG 0.429688 0.911392
125 A G U 0.42963 0.888889
126 ACP 0.428571 0.896104
127 MGQ 0.424528 0.935897
128 AR6 0.424242 0.894737
129 7DT 0.424242 0.906667
130 APR 0.424242 0.894737
131 93A 0.42268 0.833333
132 A4P 0.420168 0.869048
133 G8D 0.42 0.875
134 AD9 0.42 0.896104
135 SAP 0.42 0.873418
136 AGS 0.42 0.873418
137 CA0 0.418367 0.896104
138 ATF 0.417476 0.884615
139 AGO 0.414634 0.888889
140 A G U U 0.414286 0.888889
141 NIA 0.413043 0.82716
142 MGV 0.412844 0.890244
143 TAT 0.411765 0.884615
144 T99 0.411765 0.884615
145 ADQ 0.411215 0.871795
146 A1R 0.411215 0.839506
147 RGT 0.410714 0.909091
148 CGP 0.409836 0.86747
149 C1Z 0.409091 0.986486
150 A 0.408602 0.893333
151 AMP 0.408602 0.893333
152 UP5 0.40678 0.873418
153 AMZ 0.406593 0.918919
154 C2R 0.406593 0.906667
155 JBT 0.405882 0.778947
156 A22 0.40566 0.907895
157 25L 0.405405 0.907895
158 ADX 0.40404 0.809524
159 8OD 0.401961 0.946667
160 50T 0.4 0.883117
161 4TC 0.4 0.851852
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5O74; Ligand: GDP; Similar sites found with APoc: 136
This union binding pocket(no: 1) in the query (biounit: 5o74.bio6) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 4LC1 GDP 3.04569
2 3WYA GDP 3.33333
3 5M04 GDP 4.06091
4 1WF3 GNP 5
5 2RCN GDP 5.55556
6 4ZKD GDP 5.55556
7 1TAD GDP 6.11111
8 1TAD ALF 6.11111
9 5XKT GNP 6.11111
10 4HI0 GDP 6.11111
11 6AU6 GDP 6.11111
12 1BH2 GSP 6.11111
13 5FG3 GDP 6.66667
14 2WJG GDP 6.66667
15 1TQ4 GDP 7.1066
16 4NON GDP 7.22222
17 1PUJ GNP 7.22222
18 1SVI GDP 7.22222
19 5W75 GDP 7.22222
20 1MKY GDP 7.61421
21 5GOE GDP 7.61421
22 1SKQ GDP 7.61421
23 4DCT GDP 7.77778
24 2C78 GNP 7.77778
25 1G7S GDP 7.77778
26 2C77 GNP 7.77778
27 1D2E GDP 8.12183
28 3U6B GDP 8.33333
29 3TK1 GDP 8.33333
30 1D8T GDP 8.33333
31 2HCJ GDP 8.33333
32 4P3Y GDP 8.33333
33 5JBQ GDP 8.33333
34 4G5G GDP 8.33333
35 3U6K GDP 8.33333
36 3MD0 GDP 8.33333
37 5CK5 GDP 8.88889
38 3WXM GTP 10
39 1YRB GDP 10.5556
40 3EC1 GDP 11.1111
41 5W7Q GDP 11.6751
42 5W76 GDP 11.6751
43 4J0Q GDP 13.198
44 2ODE ALF GDP 14.1844
45 3CX8 GSP 14.2132
46 6G14 G4P 16.6667
47 5HCN GCP 17.6245
48 4RD0 GDP 20
49 4B47 GDP 21.6667
50 4BAS GNP 30
51 3T1O GDP 30.303
52 3VMF GTP 30.4569
53 3T12 GDP ALF 31.6176
54 1ZD9 GDP 31.6667
55 2X77 GDP 31.746
56 1YZG GDP 32.9609
57 4M9Q GNP 33.3333
58 1KK1 GNP 33.3333
59 1ZJ6 G3D 34.4444
60 4YLG GDP 34.6821
61 1E96 GTP 35
62 2QN6 GDP 35.4839
63 4V0K GDP 35.503
64 1KSH GDP 35.5556
65 1I4D GDP 35.5556
66 3DOE GTP 35.5556
67 1DS6 GDP 35.5556
68 1MH1 GNP 35.5556
69 2W2X GSP 35.5556
70 2WKQ GTP 36.1111
71 1G4U GDP 36.1111
72 2FJU GSP 36.5169
73 3AQ4 GDP 36.6667
74 1MR3 G3D 37.2222
75 2W83 GTP 37.5758
76 1FZQ GDP 37.7778
77 4ZI2 GNP 37.7778
78 5KUT GDP 37.7778
79 1RYH GNP 37.7778
80 5YT0 GDP 38.0952
81 3PCR GTP 38.2716
82 2ZEJ GDP 38.8889
83 3N5C GDP 38.8889
84 1O3Y GTP 40.9639
85 1J2J GTP 40.9639
86 5XC5 GTP 42.0455
87 1S9D GDP 42.0732
88 1RE0 GDP 42.0732
89 1UPT GTP 43.8596
90 5EE5 GTP 44.4444
91 3Q85 GNP 45.5621
92 1R4A GNP 46.0606
93 5UPK GNP 46.1111
94 5HPY GDP 46.6667
95 4DID GDP 46.6667
96 4YC7 GNP 46.6667
97 2NGR GDP 46.6667
98 2WMO GTP 46.6667
99 3WY9 GDP 46.875
100 4XSH GSP 46.9274
101 4U5X GNP 47.191
102 3T5G GDP 47.2222
103 3LXR GDP 47.2222
104 6BCB GSP 47.2222
105 6BCA GSP 47.2222
106 2GCN GDP 47.2222
107 6BC0 GSP 47.2222
108 3Q72 GNP 48.1928
109 3E5H GNP 48.3146
110 3GJ8 GDP 48.8889
111 3GJ4 GDP 48.8889
112 3GJ7 GDP 48.8889
113 3GJ5 GDP 48.8889
114 2HT6 GDP 49.4253
115 3GJ0 GDP 49.4444
116 3GJ3 GDP 49.4444
117 3CH5 GDP 49.4444
118 5BXQ GDP 49.4444
119 3WYF GTP 49.4444
120 5UWQ GNP 49.4444
121 5UWO GNP 49.4444
122 5UWS GNP 49.4444
123 5UWW GNP 49.4444
124 5UWP GNP 49.4444
125 5UWR GNP 49.4444
126 6CIT GNP 49.4444
127 5UWU GNP 49.4444
128 5UWJ GNP 49.4444
129 5DIF GNP 49.4444
130 5UWI GNP 49.4444
131 5UWH GNP 49.4444
132 4HAT GNP 49.4444
133 5UWT GNP 49.4444
134 5DHF GNP 49.4444
135 3WYG GTP 49.4444
136 3M1I GTP 49.4444
Pocket No.: 2; Query (leader) PDB : 5O74; Ligand: GDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5o74.bio4) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5O74; Ligand: GDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5o74.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5O74; Ligand: GDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5o74.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5O74; Ligand: GDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 5o74.bio5) has 14 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 5O74; Ligand: GDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5o74.bio3) has 16 residues
No: Leader PDB Ligand Sequence Similarity
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