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 209 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 175 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 149 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: 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
Ligand no: 2; Ligand: GER; Similar ligands found: 9
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 FOH 0.628571 0.695652
6 64Z 0.514286 0.652174
7 CTV 0.447368 0.684211
8 28U 0.444444 0.615385
9 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: 82
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 2HCJ GDP 4.83092
7 1KK1 GNP 5.31401
8 2RCN GDP 5.7971
9 1TQ4 GDP 5.7971
10 4DCT GDP 7.24638
11 5H7J GCP 9.17874
12 1YRB GDP 11.1111
13 5CK5 GDP 11.1111
14 5HCN GCP 12.0773
15 4RD0 GDP 14.0097
16 4J0Q GDP 15.4589
17 5W75 GDP 17.3913
18 4B47 GDP 17.3913
19 2X77 GDP 20.1058
20 1MKY GDP 20.2899
21 3DOE GTP 20.8333
22 1KSH GDP 21.5054
23 3WY9 GDP 25
24 4M9Q GNP 28.5024
25 1FZQ GDP 29.8343
26 2WKQ GTP 30.9179
27 4YLG GDP 31.7919
28 3N5C GDP 32.716
29 1RYH GNP 33.0049
30 1E96 GTP 33.3333
31 5FG3 GDP 33.8164
32 1I4D GDP 33.8542
33 5YT0 GDP 34.2995
34 1NF3 GNP 34.359
35 1MH1 GNP 34.4086
36 4DID GDP 35.2332
37 2NGR GDP 35.6021
38 1GRN GDP 35.6021
39 2FJU GSP 35.9551
40 5EE5 GTP 37.4269
41 4YC7 GNP 37.5691
42 2GCN GDP 42.2886
43 1DS6 GDP 42.7083
44 2CJW GDP 43.2292
45 2W2X GSP 43.7838
46 3WYF GTP 43.9614
47 3M1I GTP 43.9614
48 1OW3 GDP 44.0415
49 3T5G GDP 45.3039
50 3Q72 GNP 45.7831
51 3GJ4 GDP 45.8937
52 3GJ7 GDP 45.8937
53 3GJ5 GDP 45.8937
54 2J0V GDP 45.8937
55 3GJ8 GDP 45.8937
56 5BXQ GDP 46.3768
57 5UWP GNP 46.3768
58 5UWQ GNP 46.3768
59 5DIF GNP 46.3768
60 4HAT GNP 46.3768
61 5UWU GNP 46.3768
62 5UWW GNP 46.3768
63 6CIT GNP 46.3768
64 5UWI GNP 46.3768
65 5UWR GNP 46.3768
66 5UWS GNP 46.3768
67 5DHF GNP 46.3768
68 5UWH GNP 46.3768
69 5UWT GNP 46.3768
70 3GJ3 GDP 46.3768
71 3CH5 GDP 46.3768
72 3GJ0 GDP 46.3768
73 4D0N GDP 46.4865
74 3LXR GDP 46.4865
75 6BCA GSP 46.4865
76 2HT6 GDP 46.5517
77 4XOI GTP 46.6667
78 4XSH GSP 46.9274
79 3Q85 GNP 48.5207
80 2G77 GDP 48.9899
81 3E5H GNP 49.4382
82 5SZH GNP 49.7537
83 5UWO GNP 50
84 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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