Receptor
PDB id Resolution Class Description Source Keywords
1VG0 2.2 Å NON-ENZYME: TRANSPORT THE CRYSTAL STRUCTURES OF THE REP-1 PROTEIN IN COMPLEX WITH MONOPRENYLATED RAB7 PROTEIN RATTUS NORVEGICUS RAB PRENYLATION POST-TRANSLATIONAL MODIFICATION PROTEIN BIPROTEIN TRANSPORT COMPLEX
Ref.: STRUCTURE OF THE RAB7:REP-1 COMPLEX: INSIGHTS INTO MECHANISM OF RAB PRENYLATION AND CHOROIDEREMIA DISE CELL(CAMBRIDGE,MASS.) V. 117 749 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:3001;
Invalid;
none;
submit data
35.453 Cl [Cl-]
GDP B:1557;
Valid;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
GER A:952;
Valid;
none;
Kd = 0.8 nM
274.484 C20 H34 CC=C(...
MG B:3000;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
PG4 B:5502;
Invalid;
none;
submit data
194.226 C8 H18 O5 C(COC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1VG0 2.2 Å NON-ENZYME: TRANSPORT THE CRYSTAL STRUCTURES OF THE REP-1 PROTEIN IN COMPLEX WITH MONOPRENYLATED RAB7 PROTEIN RATTUS NORVEGICUS RAB PRENYLATION POST-TRANSLATIONAL MODIFICATION PROTEIN BIPROTEIN TRANSPORT COMPLEX
Ref.: STRUCTURE OF THE RAB7:REP-1 COMPLEX: INSIGHTS INTO MECHANISM OF RAB PRENYLATION AND CHOROIDEREMIA DISE CELL(CAMBRIDGE,MASS.) V. 117 749 2004
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 220 families.
1 1VG0 Kd = 0.8 nM GER C20 H34 CC=C(/C)CC....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 186 families.
1 1VG0 Kd = 0.8 nM GER C20 H34 CC=C(/C)CC....
2 1VG9 - GDP C10 H15 N5 O11 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 157 families.
1 1VG0 Kd = 0.8 nM GER C20 H34 CC=C(/C)CC....
2 1VG9 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; 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
Ligand no: 2; Ligand: GER; Similar ligands found: 11
No: Ligand ECFP6 Tc MDL keys Tc
1 GER 1 1
2 FAR 1 1
3 650 0.785714 0.8125
4 SQL 0.709677 0.941176
5 FOF 0.628571 0.695652
6 FOH 0.628571 0.695652
7 N1S 0.628571 0.695652
8 64Z 0.514286 0.652174
9 CTV 0.447368 0.684211
10 28U 0.444444 0.615385
11 GRQ 0.421053 0.722222
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1VG0; Ligand: GDP; Similar sites found with APoc: 133
This union binding pocket(no: 1) in the query (biounit: 1vg0.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 1SKQ GDP 3.38164
2 3EC1 GDP 4.33604
3 5W76 GDP 4.41558
4 3U6B GDP 4.83092
5 1D8T GDP 4.83092
6 1D8T GDP 4.83092
7 3U6B GDP 4.83092
8 2HCJ GDP 4.83092
9 3U6K GDP 4.83092
10 1KK1 GNP 5.31401
11 2RCN GDP 5.7971
12 2RCN GDP 5.7971
13 1TQ4 GDP 5.7971
14 4DCT GDP 7.24638
15 4DCT GDP 7.24638
16 5H7J GCP 9.17874
17 1YRB GDP 11.1111
18 5CK5 GDP 11.1111
19 5CK5 GDP 11.1111
20 1YRB GDP 11.1111
21 5HCN GCP 12.0773
22 4RD0 GDP 14.0097
23 4J0Q GDP 15.4589
24 5W75 GDP 17.3913
25 4B47 GDP 17.3913
26 2FH5 GTP 19.3237
27 2FH5 GTP 19.3237
28 2X77 GDP 20.1058
29 2X77 GDP 20.1058
30 1MKY GDP 20.2899
31 3DOE GTP 20.8333
32 1KSH GDP 21.5054
33 3WY9 GDP 25
34 3WY9 GDP 25
35 4GOJ GNP 28.0423
36 4ZI2 GNP 28.4211
37 4M9Q GNP 28.5024
38 4M9Q GNP 28.5024
39 4M9Q GNP 28.5024
40 1FZQ GDP 29.8343
41 2WKQ GTP 30.9179
42 4YLG GDP 31.7919
43 3N5C GDP 32.716
44 1RYH GNP 33.0049
45 1E96 GTP 33.3333
46 5FG3 GDP 33.8164
47 4NCN GTP 33.8164
48 4TMZ GSP 33.8164
49 1I4D GDP 33.8542
50 5YT0 GDP 34.2995
51 1NF3 GNP 34.359
52 1NF3 GNP 34.359
53 1MH1 GNP 34.4086
54 3SBD GNP 34.7594
55 4DID GDP 35.2332
56 2NGR GDP 35.6021
57 1GRN GDP 35.6021
58 2FJU GSP 35.9551
59 1HE1 GDP 36.3636
60 5EE5 GTP 37.4269
61 4YC7 GNP 37.5691
62 2GCN GDP 42.2886
63 2GCO GNP 42.2886
64 1DS6 GDP 42.7083
65 2CJW GDP 43.2292
66 2CJW GDP 43.2292
67 2W2X GSP 43.7838
68 2W2X GSP 43.7838
69 3WYF GTP 43.9614
70 3WYF GTP 43.9614
71 3M1I GTP 43.9614
72 1OW3 GDP 44.0415
73 3T5G GDP 45.3039
74 3Q72 GNP 45.7831
75 3Q72 GNP 45.7831
76 3GJ4 GDP 45.8937
77 3GJ7 GDP 45.8937
78 3GJ5 GDP 45.8937
79 2J0V GDP 45.8937
80 2J0V GDP 45.8937
81 3GJX GTP 45.8937
82 3GJ8 GDP 45.8937
83 3GJ8 GDP 45.8937
84 3GJ5 GDP 45.8937
85 3GJ7 GDP 45.8937
86 3GJ4 GDP 45.8937
87 2J0V GDP 45.8937
88 2J0V GDP 45.8937
89 6SGE GTP 45.9016
90 6SGE GTP 45.9016
91 6BSX E7S 46.0674
92 6BSX GDP 46.0674
93 6BSX GDP 46.0674
94 6BSX E7S 46.0674
95 6BSX GDP 46.0674
96 5BXQ GDP 46.3768
97 5BXQ GDP 46.3768
98 5BXQ GDP 46.3768
99 5UWP GNP 46.3768
100 5UWQ GNP 46.3768
101 5DIF GNP 46.3768
102 4HAT GNP 46.3768
103 5UWU GNP 46.3768
104 5UWW GNP 46.3768
105 6CIT GNP 46.3768
106 5UWI GNP 46.3768
107 5UWR GNP 46.3768
108 5UWS GNP 46.3768
109 5DHF GNP 46.3768
110 5UWH GNP 46.3768
111 5UWT GNP 46.3768
112 1IBR GNP 46.3768
113 3GJ0 GDP 46.3768
114 3GJ3 GDP 46.3768
115 3CH5 GDP 46.3768
116 3CH5 GDP 46.3768
117 3GJ0 GDP 46.3768
118 4D0N GDP 46.4865
119 3LXR GDP 46.4865
120 6BCA GSP 46.4865
121 6BCA GSP 46.4865
122 2HT6 GDP 46.5517
123 2HT6 GDP 46.5517
124 4XOI GTP 46.6667
125 4XOI GTP 46.6667
126 4XSH GSP 46.9274
127 3Q85 GNP 48.5207
128 3Q85 GNP 48.5207
129 2G77 GDP 48.9899
130 5UQW GDP 49.2063
131 3E5H GNP 49.4382
132 3E5H GNP 49.4382
133 5SZH GNP 49.7537
134 5UWO GNP 50
135 3WYG GTP 50
Pocket No.: 2; Query (leader) PDB : 1VG0; Ligand: GER; 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: 1vg0.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
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