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;
submit data
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 209 families.
1 1YZG - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 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 1O3Y - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
5 1YZG - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
6 3N5C - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
7 1E0S - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
8 3AQ4 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 4Y0V - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
10 4YLG - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
11 1MR3 - G3D C10 H16 N5 O14 P3 c1nc2c(n1[....
50% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 204 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 3N5C - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
12 1E0S - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
13 1ZD9 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
14 2AL7 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
15 3AQ4 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
16 4Y0V - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
17 4YLG - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
18 1MR3 - G3D C10 H16 N5 O14 P3 c1nc2c(n1[....
19 4BAS - GNP C10 H17 N6 O13 P3 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
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: 106
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 4DKX GDP 2.23464
3 3WYA GDP 3.35196
4 3WY9 GDP 3.35196
5 4J0Q GDP 3.91061
6 1DAR GDP 4.46927
7 2RCN GDP 5.02793
8 5XKT GNP 5.58659
9 1G7S GDP 6.14525
10 1TQ4 GDP 6.14525
11 2CJW GDP 6.70391
12 1YRB GDP 6.70391
13 5M04 GDP 6.70391
14 4B47 GDP 6.70391
15 3EC1 GDP 6.70391
16 4PPF FLC 6.70391
17 3MD0 GDP 7.26257
18 3VMF GTP 7.26257
19 1D2E GDP 7.82123
20 2HT6 GDP 8.04598
21 2C78 GNP 8.37989
22 4LC1 GDP 8.37989
23 4P3Y GDP 8.93855
24 3U6B GDP 8.93855
25 5JBQ GDP 8.93855
26 1SKQ GDP 8.93855
27 1D8T GDP 8.93855
28 3U6K GDP 8.93855
29 4G5G GDP 8.93855
30 2HCJ GDP 8.93855
31 2BVN GNP 8.93855
32 1PUJ GNP 9.49721
33 6G14 G4P 9.49721
34 3CNL GNP 10.0559
35 1KK1 GNP 11.1732
36 3TK1 GDP 11.1732
37 4PC3 GDP 12.2905
38 5H7J GCP 13.4078
39 5H7K GDP 13.4078
40 5YT0 GDP 15.0838
41 5FG3 GDP 15.0838
42 5GOE GDP 16.2011
43 5W7Q GDP 18.9944
44 5W76 GDP 18.9944
45 1GOT GDP 20.1117
46 6AU6 GDP 20.6704
47 1CS4 GSP 20.6704
48 1TAD ALF 21.7877
49 1TAD GDP 21.7877
50 6CRK GDP 22.3464
51 1BH2 GSP 22.3464
52 1GP2 GDP 22.3464
53 5KDO GDP 22.3464
54 1Y3A GDP 22.3464
55 2EFE GNH 22.905
56 2FFQ GSP 23.3918
57 4DCT GDP 26.257
58 3Q85 GNP 27.8107
59 3WYF GTP 28.4916
60 3WYG GTP 28.4916
61 3M1I GTP 28.4916
62 3BC1 GNP 29.0503
63 3CX8 GSP 29.6089
64 3GJ3 GDP 29.6089
65 3GJ0 GDP 29.6089
66 3GJ7 GDP 29.6089
67 5UWP GNP 29.6089
68 5UWQ GNP 29.6089
69 5BXQ GDP 29.6089
70 3GJ4 GDP 29.6089
71 6CIT GNP 29.6089
72 4HAT GNP 29.6089
73 5UWU GNP 29.6089
74 5UWS GNP 29.6089
75 5DHF GNP 29.6089
76 5UWO GNP 29.6089
77 5UWT GNP 29.6089
78 3GJ8 GDP 29.6089
79 3CH5 GDP 29.6089
80 5UWH GNP 29.6089
81 3GJ5 GDP 29.6089
82 3RWO GDP 30.1676
83 3T5G GDP 30.1676
84 1GUA GNP 30.5389
85 3Q72 GNP 30.7229
86 2QN6 GDP 31.1828
87 5TB5 GDP 31.2849
88 1MKY GDP 31.8436
89 2C5L GTP 32.3699
90 5O74 GDP 32.9609
91 1UAD GNP 33.1429
92 5E95 GDP 33.3333
93 5CK5 GDP 33.5196
94 6D5J GNP 33.5329
95 6D5E GNP 33.5329
96 6BVJ GNP 33.5329
97 6BVK GNP 33.5329
98 6D5H GNP 33.5329
99 6D5G GNP 33.5329
100 1CLU DBG 33.7349
101 1WQ1 GDP 33.7349
102 1U8Z GDP 34.5238
103 3SFV GDP 35.1955
104 3T12 GDP ALF 39.6648
105 3T1O GDP 39.6648
106 2QTV GNP 44.3114
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