Receptor
PDB id Resolution Class Description Source Keywords
2G77 2.26 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF GYP1 TBC DOMAIN IN COMPLEX WITH RAB33 GTPASE BOUND TO GDP AND ALF3 SACCHAROMYCES CEREVISIAE PROTEIN TRANSPORT GYP1 TBC DOMAIN RAB33 VESICULAR TRAFFICKING HYDROLASE ACTIVATOR/PROTEIN TRANSPORT COMPLEX
Ref.: TBC-DOMAIN GAPS FOR RAB GTPASES ACCELERATE GTP HYDROLYSIS BY A DUAL-FINGER MECHANISM. NATURE V. 442 303 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AF3 B:502;
Valid;
none;
submit data
83.977 Al F3 F[Al]...
GDP B:501;
Valid;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
MG B:503;
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
2G77 2.26 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF GYP1 TBC DOMAIN IN COMPLEX WITH RAB33 GTPASE BOUND TO GDP AND ALF3 SACCHAROMYCES CEREVISIAE PROTEIN TRANSPORT GYP1 TBC DOMAIN RAB33 VESICULAR TRAFFICKING HYDROLASE ACTIVATOR/PROTEIN TRANSPORT COMPLEX
Ref.: TBC-DOMAIN GAPS FOR RAB GTPASES ACCELERATE GTP HYDROLYSIS BY A DUAL-FINGER MECHANISM. NATURE V. 442 303 2006
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 283 families.
1 2G77 - 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 235 families.
1 2G77 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 193 families.
1 2G77 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: AF3; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 AF3 1 1
Ligand no: 2; Ligand: GDP; Similar ligands found: 168
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 GNP 0.839506 0.973684
6 9GM 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 GKE 0.747253 0.961039
18 GDD 0.747253 0.961039
19 GDC 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 GDR 0.72043 0.961039
26 GFB 0.72043 0.961039
27 GTG 0.72043 0.936709
28 G4P 0.715909 0.986486
29 6CK 0.712766 0.936709
30 G3A 0.712766 0.973684
31 GDP AF3 0.7 0.888889
32 GDP ALF 0.7 0.888889
33 ALF GDP 0.7 0.888889
34 YGP 0.698925 0.901235
35 JB2 0.697917 0.961039
36 GKD 0.697917 0.961039
37 GPD 0.690722 0.925
38 GDX 0.690722 0.973684
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 GDP 7MG 0.636364 0.911392
44 DGI 0.636364 0.923077
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 KB7 0.629214 0.82716
52 CG2 0.622642 0.936709
53 FEG 0.619048 0.879518
54 MGD 0.614679 0.891566
55 ZGP 0.613208 0.869048
56 GH3 0.612903 0.973333
57 3GP 0.611765 0.946667
58 MD1 0.607143 0.891566
59 PGD 0.59292 0.925
60 DGT 0.591398 0.923077
61 BGO 0.588785 0.924051
62 TPG 0.582609 0.840909
63 DBG 0.582609 0.948718
64 KBD 0.581633 0.82716
65 2GP 0.574713 0.96
66 FE9 0.570175 0.776596
67 GCP G 0.56 0.921053
68 KBJ 0.558824 0.797619
69 G A A A 0.553571 0.923077
70 A G 0.553571 0.935065
71 MGP 0.553191 0.961039
72 U A G G 0.548673 0.935065
73 G4M 0.548387 0.880952
74 6G0 0.547368 0.961039
75 G1R G1R 0.542373 0.924051
76 P2G 0.527473 0.883117
77 PGD O 0.525 0.850575
78 ADP 0.522222 0.92
79 R5I 0.520833 0.946667
80 R7I 0.520833 0.946667
81 GGM 0.517544 0.901235
82 DGP 0.516484 0.910256
83 DG 0.516484 0.910256
84 P1G 0.516129 0.871795
85 G U 0.513274 0.9
86 G1G 0.508475 0.925
87 IMP 0.505495 0.959459
88 AKW 0.504425 0.890244
89 G C 0.504348 0.9
90 GPC 0.491525 0.879518
91 G7M 0.483871 0.948052
92 6AD 0.479592 0.841463
93 ATP 0.473684 0.92
94 HEJ 0.473684 0.92
95 G2Q 0.471154 0.961039
96 AQP 0.46875 0.92
97 5FA 0.46875 0.92
98 GTA 0.468468 0.936709
99 7DD 0.468085 0.906667
100 G G G RPC 0.466102 0.875
101 SGP 0.463158 0.82716
102 01G 0.462963 0.902439
103 JSQ 0.459184 0.873418
104 HFD 0.459184 0.873418
105 AP5 0.457447 0.894737
106 B4P 0.457447 0.894737
107 A2D 0.456522 0.894737
108 6YZ 0.455446 0.896104
109 G G G C 0.455285 0.9125
110 ANP 0.454545 0.896104
111 5GP 5GP 0.454545 0.883117
112 ACQ 0.454545 0.896104
113 AT4 0.452632 0.884615
114 A G C C 0.451613 0.911392
115 APC G U 0.45082 0.886076
116 PRT 0.449541 0.959459
117 G U34 0.449153 0.888889
118 DG DG 0.448598 0.865854
119 ITT 0.447917 0.868421
120 BA3 0.446809 0.894737
121 35G 0.444444 0.933333
122 PCG 0.444444 0.933333
123 C2E 0.444444 0.921053
124 MGO 0.441176 0.864198
125 AN2 0.4375 0.907895
126 G C C C 0.4375 0.924051
127 NO7 0.436893 0.860759
128 M33 0.43299 0.883117
129 UCG 0.429688 0.911392
130 A G U 0.42963 0.888889
131 ACP 0.428571 0.896104
132 MGQ 0.424528 0.935897
133 7DT 0.424242 0.906667
134 APR 0.424242 0.894737
135 AR6 0.424242 0.894737
136 93A 0.42268 0.833333
137 A4P 0.420168 0.869048
138 AGS 0.42 0.873418
139 AD9 0.42 0.896104
140 G8D 0.42 0.875
141 SAP 0.42 0.873418
142 CA0 0.418367 0.896104
143 ATF 0.417476 0.884615
144 AGO 0.414634 0.888889
145 A G U U 0.414286 0.888889
146 KG4 0.414141 0.896104
147 NIA 0.413043 0.82716
148 MGV 0.412844 0.890244
149 T99 0.411765 0.884615
150 TAT 0.411765 0.884615
151 A1R 0.411215 0.839506
152 ADQ 0.411215 0.871795
153 RGT 0.410714 0.909091
154 CGP 0.409836 0.86747
155 HQG 0.409524 0.907895
156 C1Z 0.409091 0.986486
157 AMP 0.408602 0.893333
158 A 0.408602 0.893333
159 UP5 0.40678 0.873418
160 C2R 0.406593 0.906667
161 AMZ 0.406593 0.918919
162 JBT 0.405882 0.778947
163 A22 0.40566 0.907895
164 25L 0.405405 0.907895
165 ADX 0.40404 0.809524
166 8OD 0.401961 0.946667
167 4TC 0.4 0.851852
168 50T 0.4 0.883117
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2G77; Ligand: GDP; Similar sites found with APoc: 187
This union binding pocket(no: 1) in the query (biounit: 2g77.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 3U6B GDP 1.77665
2 3U6K GDP 1.77665
3 2BVN GNP 1.78117
4 1D8T GDP 1.78117
5 5W75 GDP 2.04082
6 5W75 GDP 2.04082
7 5W75 GDP 2.04082
8 5W75 GDP 2.04082
9 2HCJ GDP 2.08955
10 5W76 GDP 2.52525
11 2C78 GNP 3.20988
12 1KK1 GNP 3.53535
13 2RCN GDP 4.18994
14 2RCN GDP 4.18994
15 3WY9 GDP 4.54545
16 3WYA GDP 4.54545
17 2C77 GNP 4.69136
18 4NCN GTP 5.55556
19 3WXM GTP 5.55556
20 3WXM GTP 5.55556
21 3WXM GTP 5.55556
22 1SKQ GDP 6.06061
23 5H7J GCP 6.06061
24 2QN6 GDP 6.45161
25 1CS4 GSP 6.56566
26 5FG3 GDP 6.58106
27 4J0Q GDP 7.07071
28 4J0Q GDP 7.07071
29 4J0Q GDP 7.07071
30 4J0Q GDP 7.07071
31 4J0Q GDP 7.07071
32 5YT0 GDP 7.14286
33 2XTZ GSP 8.08081
34 2XTZ GSP 8.08081
35 2XTZ GSP 8.08081
36 1YRB GDP 8.58586
37 1YRB GDP 8.58586
38 4ZKD GDP 8.78049
39 3VMF GTP 9.09091
40 4DCT GDP 10.101
41 4DCT GDP 10.101
42 5H7K GDP 12.6263
43 4B47 GDP 12.6722
44 1NRJ GTP 16.6667
45 5CK5 GDP 17.6768
46 5CK5 GDP 17.6768
47 5CK5 GDP 17.6768
48 1MKY GDP 20.7071
49 1UPT GTP 23.3918
50 1UPT GTP 23.3918
51 1UPT GTP 23.3918
52 1UPT GTP 23.3918
53 1F6B GDP 25.2525
54 1F6B GDP 25.2525
55 4M9Q GNP 27.2727
56 4M9Q GNP 27.2727
57 4M9Q GNP 27.2727
58 2FH5 GTP 27.7778
59 2FH5 GTP 27.7778
60 2FH5 GTP 27.7778
61 5DI3 GNP 28.6486
62 5DI3 GNP 28.6486
63 1M2O GNP 28.9474
64 1M2O GNP 28.9474
65 1M2O GNP 28.9474
66 4ZI2 GNP 30.5263
67 4ZI2 GNP 30.5263
68 4GOJ GNP 30.6878
69 4GOJ GNP 30.6878
70 1DS6 GDP 30.7292
71 1E96 GTP 30.7292
72 2WKQ GTP 30.8081
73 1I4D GDP 31.25
74 1FZQ GDP 32.0442
75 1MH1 GNP 32.2581
76 3DOE GTP 32.2917
77 1RYH GNP 32.3232
78 3SBD GNP 32.6203
79 2QTV GNP 32.9341
80 2W2X GSP 32.973
81 2W2X GSP 32.973
82 1ZJ6 G3D 33.1551
83 1KSH GDP 33.3333
84 1ZD9 GDP 33.5106
85 2FJU GSP 33.7079
86 2J0V GDP 33.8384
87 2J0V GDP 33.8384
88 2J0V GDP 33.8384
89 2J0V GDP 33.8384
90 1HE1 GDP 34.0909
91 4DID GDP 34.8485
92 1O3Y GTP 34.9398
93 1J2J GTP 34.9398
94 2J59 GTP 34.9398
95 2J59 GTP 34.9398
96 2J59 GTP 34.9398
97 2J59 GTP 34.9398
98 1O3Y GTP 34.9398
99 3E5H GNP 35.3933
100 2CJW GDP 35.4167
101 2CJW GDP 35.4167
102 1RE0 GDP 35.9756
103 2GCO GNP 36.3636
104 5UPK GNP 36.8687
105 1M7B GTP 36.9565
106 1GWN GTP 37.0732
107 1GWN GTP 37.0732
108 6R3V GDP 37.8238
109 5HPY GDP 38.9189
110 5HPY GDP 38.9189
111 2W83 GTP 39.3939
112 2W83 GTP 39.3939
113 2W83 GTP 39.3939
114 4XOI GTP 39.4444
115 4XOI GTP 39.4444
116 4D0N GDP 39.4595
117 3LXR GDP 39.4595
118 6BCA GSP 39.4595
119 6BC0 GSP 39.4595
120 2HT6 GDP 39.6552
121 2HT6 GDP 39.6552
122 6SGE GTP 39.8907
123 6SGE GTP 39.8907
124 3GJ4 GDP 39.899
125 3GJ7 GDP 39.899
126 3GJ5 GDP 39.899
127 3GJX GTP 39.899
128 3CH5 GDP 40.404
129 5UWQ GNP 40.404
130 5UWP GNP 40.404
131 5UWO GNP 40.404
132 5UWU GNP 40.404
133 5DIF GNP 40.404
134 4HAT GNP 40.404
135 5UWH GNP 40.404
136 5UWW GNP 40.404
137 6CIT GNP 40.404
138 5UWI GNP 40.404
139 5UWT GNP 40.404
140 5UWR GNP 40.404
141 5DHF GNP 40.404
142 5UWS GNP 40.404
143 3N5C GDP 40.7407
144 3Q85 GNP 41.4201
145 3Q85 GNP 41.4201
146 3M1I GTP 42.4242
147 3WYF GTP 42.4242
148 3WYF GTP 42.4242
149 4DKX GDP 43.9394
150 4DKX GDP 43.9394
151 6HDU GTP 44.5652
152 6HDU GTP 44.5652
153 6HDU GTP 44.5652
154 3T5G GDP 44.7514
155 5LEF GTP 45.0262
156 5LEF GTP 45.0262
157 5EE5 GTP 45.0292
158 1WA5 GTP 45.4545
159 6BSX E7S 45.5056
160 6BSX GDP 45.5056
161 6BSX E7S 45.5056
162 6BSX GDP 45.5056
163 6BSX GDP 45.5056
164 3WYG GTP 46.1538
165 3Q72 GNP 47.5904
166 3Q72 GNP 47.5904
167 1R4A GNP 47.8788
168 1R4A GNP 47.8788
169 1R4A GNP 47.8788
170 1R4A GNP 47.8788
171 6IYB GTP 47.9798
172 5TB5 GDP 48.1081
173 5TAR GDP 48.1081
174 5TB5 GDP 48.1081
175 3BC1 GNP 48.7179
176 3BC1 GNP 48.7179
177 1X1R GDP 48.8764
178 1VG8 GNP 48.9899
179 1VG8 GNP 48.9899
180 1VG8 GNP 48.9899
181 1VG0 GDP 48.9899
182 2Y8E GNP 49.7207
183 2Y8E GNP 49.7207
184 2Y8E GNP 49.7207
185 2EFE GNH 49.7238
186 2EFE GNH 49.7238
187 5UQW GDP 49.7355
Pocket No.: 2; Query (leader) PDB : 2G77; Ligand: AF3; Similar sites found with APoc: 36
This union binding pocket(no: 2) in the query (biounit: 2g77.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 1CS4 GSP 6.56566
2 4ZKD GDP 8.78049
3 1FQJ ALF 21.7687
4 1FQJ ALF 21.7687
5 4M9Q GNP 27.2727
6 4BAS GNP 30.303
7 4BAS GNP 30.303
8 2W2X GSP 32.973
9 1M7B GTP 36.9565
10 1GWN GTP 37.0732
11 1GWN GTP 37.0732
12 6BCA GSP 39.4595
13 6SGE GTP 39.8907
14 6SGE GTP 39.8907
15 5UWQ GNP 40.404
16 5UWP GNP 40.404
17 5UWU GNP 40.404
18 5UWT GNP 40.404
19 5UWI GNP 40.404
20 4HAT GNP 40.404
21 5UWO GNP 40.404
22 5UWR GNP 40.404
23 5UWS GNP 40.404
24 5UWH GNP 40.404
25 5DIF GNP 40.404
26 5LEF GTP 45.0262
27 5LEF GTP 45.0262
28 6IYB GTP 47.9798
29 3BC1 GNP 48.7179
30 3BC1 GNP 48.7179
31 1VG8 GNP 48.9899
32 1VG8 GNP 48.9899
33 1VG8 GNP 48.9899
34 2Y8E GNP 49.7207
35 2Y8E GNP 49.7207
36 2Y8E GNP 49.7207
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