Receptor
PDB id Resolution Class Description Source Keywords
1YZG 2 Å NON-ENZYME: TRANSPORT STRUCTURE OF HUMAN ADP-RIBOSYLATION FACTOR-LIKE 8 HOMO SAPIENS TRANSPORT PROTEIN; GDP-BINDING; MEMBRANE TRAFFICKING STRUCTGENOMICS PSI PROTEIN STRUCTURE INITIATIVE STRUCTURAL GENCONSORTIUM SGC TRANSPORT PROTEIN
Ref.: STRUCTURE OF HUMAN ADP-RIBOSYLATION FACTOR-LIKE 8 TO BE PUBLISHED 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:181;
Valid;
none;
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443.201 C10 H15 N5 O11 P2 c1nc2...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1YZG 2 Å NON-ENZYME: TRANSPORT STRUCTURE OF HUMAN ADP-RIBOSYLATION FACTOR-LIKE 8 HOMO SAPIENS TRANSPORT PROTEIN; GDP-BINDING; MEMBRANE TRAFFICKING STRUCTGENOMICS PSI PROTEIN STRUCTURE INITIATIVE STRUCTURAL GENCONSORTIUM SGC TRANSPORT PROTEIN
Ref.: STRUCTURE OF HUMAN ADP-RIBOSYLATION FACTOR-LIKE 8 TO BE PUBLISHED 2005
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 220 families.
1 1YZG - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1312 families.
1 2X77 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 1RRG - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 1HUR - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 1YZG - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 3N5C - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
6 1E0S - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
7 3AQ4 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
8 4Y0V - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 1MR3 - G3D C10 H16 N5 O14 P3 c1nc2c(n1[....
50% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 218 families.
1 4V0K - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 4V0L - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
3 2X77 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 1RRG - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 1HUR - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
6 1O3Y - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
7 1FZQ Kd = 24 nM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
8 1Z6Y - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 1ZJ6 - G3D C10 H16 N5 O14 P3 c1nc2c(n1[....
10 1YZG - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
11 6A8D - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
12 3N5C - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
13 1E0S - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
14 1ZD9 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
15 2AL7 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
16 3AQ4 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
17 4Y0V - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
18 4YLG - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
19 1MR3 - G3D C10 H16 N5 O14 P3 c1nc2c(n1[....
20 4BAS - GNP C10 H17 N6 O13 P3 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
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1YZG; Ligand: GDP; Similar sites found with APoc: 211
This union binding pocket(no: 1) in the query (biounit: 1yzg.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 5W75 GDP 1.67598
2 5W75 GDP 1.67598
3 5W75 GDP 1.67598
4 5W75 GDP 1.67598
5 4DKX GDP 2.23464
6 4DKX GDP 2.23464
7 3WYA GDP 3.35196
8 3WY9 GDP 3.35196
9 3WY9 GDP 3.35196
10 4J0Q GDP 3.91061
11 4J0Q GDP 3.91061
12 4J0Q GDP 3.91061
13 4J0Q GDP 3.91061
14 4J0Q GDP 3.91061
15 1DAR GDP 4.46927
16 6JFK GDP 4.46927
17 2RCN GDP 5.02793
18 2RCN GDP 5.02793
19 5XKT GNP 5.58659
20 5XKT GNP 5.58659
21 1G7S GDP 6.14525
22 1TQ4 GDP 6.14525
23 2CJW GDP 6.70391
24 2CJW GDP 6.70391
25 1YRB GDP 6.70391
26 5M04 GDP 6.70391
27 4B47 GDP 6.70391
28 3EC1 GDP 6.70391
29 3EC1 GDP 6.70391
30 4PPF FLC 6.70391
31 3MD0 GDP 7.26257
32 3VMF GTP 7.26257
33 1D2E GDP 7.82123
34 1D2E GDP 7.82123
35 1D2E GDP 7.82123
36 1D2E GDP 7.82123
37 3WXM GTP 7.82123
38 3WXM GTP 7.82123
39 3WXM GTP 7.82123
40 2HT6 GDP 8.04598
41 2HT6 GDP 8.04598
42 2C78 GNP 8.37989
43 4LC1 GDP 8.37989
44 4LC1 GDP 8.37989
45 3U6B GDP 8.93855
46 4P3Y GDP 8.93855
47 3U6B GDP 8.93855
48 5JBQ GDP 8.93855
49 1SKQ GDP 8.93855
50 1D8T GDP 8.93855
51 3U6K GDP 8.93855
52 1SKQ GDP 8.93855
53 1D8T GDP 8.93855
54 2BVN GNP 8.93855
55 4G5G GDP 8.93855
56 2HCJ GDP 8.93855
57 3U6K GDP 8.93855
58 2BVN GNP 8.93855
59 6G14 G4P 9.49721
60 1PUJ GNP 9.49721
61 6G14 G4P 9.49721
62 3CNL GNP 10.0559
63 2AWN ADP 10.0559
64 1KK1 GNP 11.1732
65 3TK1 GDP 11.1732
66 3TK1 GDP 11.1732
67 4PC3 GDP 12.2905
68 4PC3 GDP 12.2905
69 5H7J GCP 13.4078
70 5H7K GDP 13.4078
71 5YT0 GDP 15.0838
72 5FG3 GDP 15.0838
73 5GOE GDP 16.2011
74 5W7Q GDP 18.9944
75 5W76 GDP 18.9944
76 2XTZ GSP 18.9944
77 1GOT GDP 20.1117
78 6AU6 GDP 20.6704
79 1CS4 GSP 20.6704
80 6FF8 GTP 20.6704
81 1TAD GDP 21.7877
82 1TAD ALF 21.7877
83 6MHE GDP 21.7877
84 1FQJ GDP 22.3464
85 6CRK GDP 22.3464
86 1BH2 GSP 22.3464
87 1GP2 GDP 22.3464
88 5KDO GDP 22.3464
89 1Y3A GDP 22.3464
90 1FQK GDP 22.3464
91 1Y3A GDP 22.3464
92 2OM2 GDP 22.3464
93 3QBT GNP 22.4138
94 3QBT GNP 22.4138
95 4LHW GNP 22.4138
96 4LHW GNP 22.4138
97 2EFE GNH 22.905
98 2EFE GNH 22.905
99 2FFQ GSP 23.3918
100 2Y8E GNP 23.4637
101 2Y8E GNP 23.4637
102 2Y8E GNP 23.4637
103 4DCT GDP 26.257
104 3Q85 GNP 27.8107
105 3Q85 GNP 27.8107
106 3WYF GTP 28.4916
107 3WYG GTP 28.4916
108 3M1I GTP 28.4916
109 3WYF GTP 28.4916
110 3MJH GTP 28.5714
111 1TU3 GNP 28.655
112 1TU3 GNP 28.655
113 1TU3 GNP 28.655
114 3BC1 GNP 29.0503
115 3BC1 GNP 29.0503
116 3GJX GTP 29.0503
117 3CX8 GSP 29.6089
118 5BXQ GDP 29.6089
119 5BXQ GDP 29.6089
120 3GJ5 GDP 29.6089
121 3GJ3 GDP 29.6089
122 3GJ0 GDP 29.6089
123 3GJ7 GDP 29.6089
124 5UWP GNP 29.6089
125 5UWQ GNP 29.6089
126 5BXQ GDP 29.6089
127 3GJ4 GDP 29.6089
128 6CIT GNP 29.6089
129 4HAT GNP 29.6089
130 5UWU GNP 29.6089
131 5UWS GNP 29.6089
132 5DHF GNP 29.6089
133 5UWO GNP 29.6089
134 5UWT GNP 29.6089
135 3GJ8 GDP 29.6089
136 3CH5 GDP 29.6089
137 3CH5 GDP 29.6089
138 5UWH GNP 29.6089
139 3GJ8 GDP 29.6089
140 3GJ5 GDP 29.6089
141 3GJ7 GDP 29.6089
142 1IBR GNP 29.6089
143 3GJ4 GDP 29.6089
144 3GJ0 GDP 29.6089
145 3AB3 GDP 29.6089
146 3E5H GNP 29.7753
147 3RWO GDP 30.1676
148 3RWO GDP 30.1676
149 3T5G GDP 30.1676
150 4KVG GTP 30.3571
151 1GUA GNP 30.5389
152 3Q72 GNP 30.7229
153 3Q72 GNP 30.7229
154 6HH2 GDP 30.7263
155 2QN6 GDP 31.1828
156 5UQW GDP 31.2849
157 5TB5 GDP 31.2849
158 6BSX GDP 31.4607
159 6BSX E7S 31.4607
160 5Z2M GTP 31.8182
161 1MKY GDP 31.8436
162 6FA3 GNP 31.9767
163 6FA3 GNP 31.9767
164 6FA3 GNP 31.9767
165 2C5L GTP 32.3699
166 2C5L GTP 32.3699
167 2HV8 GTP 32.5581
168 1ZC3 GNP 32.5714
169 4K81 GTP 32.7485
170 4K81 GTP 32.7485
171 2D7C GTP 32.9341
172 5WHA GDP 32.9412
173 5WHA GDP 32.9412
174 5O74 GDP 32.9609
175 5O74 GDP 32.9609
176 5O74 GDP 32.9609
177 5O74 GDP 32.9609
178 5O74 GDP 32.9609
179 6HDU GTP 32.9609
180 6HDU GTP 32.9609
181 1UAD GNP 33.1429
182 1UAD GNP 33.1429
183 5E95 GDP 33.3333
184 5WDR GNP 33.3333
185 5CK5 GDP 33.5196
186 5CK5 GDP 33.5196
187 5CK5 GDP 33.5196
188 6D5J GNP 33.5329
189 6D5E GNP 33.5329
190 6BVJ GNP 33.5329
191 6BVK GNP 33.5329
192 6D5H GNP 33.5329
193 6D5G GNP 33.5329
194 3NKV GNP 33.7143
195 1CLU DBG 33.7349
196 5WLB GNP 33.7349
197 1WQ1 GDP 33.7349
198 1NVV GNP 33.7349
199 3DDC GNP 33.7349
200 1U8Z GDP 34.5238
201 1U8Z GDP 34.5238
202 2FH5 GTP 35.1955
203 2FH5 GTP 35.1955
204 3SFV GDP 35.1955
205 3T12 GDP ALF 39.6648
206 3T1O GDP 39.6648
207 3T1O GDP 39.6648
208 2BME GNP 39.6648
209 2BME GNP 39.6648
210 2QTV GNP 44.3114
211 4M9Q GNP 46.3687
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