Receptor
PDB id Resolution Class Description Source Keywords
1R8S 1.46 Å NON-ENZYME: TRANSPORT ARF1[DELTA1-17]-GDP IN COMPLEX WITH A SEC7 DOMAIN CARRYING T MUTATION OF THE CATALYTIC GLUTAMATE TO LYSINE BOS TAURUS PROTEIN TRANSPORT/EXCHANGE FACTOR PROTEIN TRANSPORT-EXCHANGCOMPLEX
Ref.: STRUCTURAL SNAPSHOTS OF THE MECHANISM AND INHIBITIO GUANINE NUCLEOTIDE EXCHANGE FACTOR NATURE V. 426 525 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BME A:506;
Invalid;
none;
submit data
78.133 C2 H6 O S C(CS)...
FMT A:503;
A:504;
E:505;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
46.025 C H2 O2 C(=O)...
GDP A:401;
Valid;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
SO3 E:502;
Invalid;
none;
submit data
80.063 O3 S [O-]S...
SO4 E:501;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1S9D 1.8 Å NON-ENZYME: TRANSPORT ARF1[DELTA 1-17]-GDP-MG IN COMPLEX WITH BREFELDIN A AND A SE BOS TAURUS PROTEIN TRANSPORT/EXCHANGE FACTOR PROTEIN TRANSPORT-EXCHANGCOMPLEX
Ref.: STRUCTURAL SNAPSHOTS OF THE MECHANISM AND INHIBITIO GUANINE NUCLEOTIDE EXCHANGE FACTOR NATURE V. 426 525 2003
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 209 families.
1 1R8S - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 1S9D - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 1R8Q - G3D C10 H16 N5 O14 P3 c1nc2c(n1[....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 175 families.
1 1R8S - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 1S9D - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 1R8Q - G3D C10 H16 N5 O14 P3 c1nc2c(n1[....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 149 families.
1 1R8S - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 1S9D - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 1R8Q - G3D C10 H16 N5 O14 P3 c1nc2c(n1[....
4 2R09 - 4IP C6 H16 O18 P4 [C@H]1([C@....
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 : 1S9D; Ligand: GDP; Similar sites found with APoc: 71
This union binding pocket(no: 1) in the query (biounit: 1s9d.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 1DAR GDP 3.94089
2 5W7Q GDP 4.87805
3 5W76 GDP 5.41872
4 5YT0 GDP 5.4878
5 1SKQ GDP 6.09756
6 2RCN GDP 6.70732
7 3U6B GDP 6.89655
8 2HCJ GDP 6.89655
9 5JBQ GDP 6.89655
10 1D8T GDP 6.89655
11 4G5G GDP 6.89655
12 3U6K GDP 6.89655
13 2BVN GNP 6.89655
14 3MD0 GDP 7.04225
15 1MKY GDP 7.31707
16 5W75 GDP 7.31707
17 5H7J GCP 7.38916
18 5H7K GDP 7.38916
19 4J0Q GDP 7.92683
20 5FG3 GDP 8.53659
21 2AWN ADP 9.14634
22 1KK1 GNP 9.7561
23 3CNL GNP 9.7561
24 5CK5 GDP 9.7561
25 4DKX GDP 9.85222
26 1G7S GDP 10.3448
27 4LC1 GDP 10.3448
28 1PUJ GNP 10.3659
29 6G14 G4P 10.3659
30 1YRB GDP 10.8374
31 4P3Y GDP 11.5385
32 3WYA GDP 11.8227
33 3WY9 GDP 11.8227
34 5GOE GDP 11.8227
35 3TK1 GDP 12.8049
36 4B47 GDP 13.2231
37 1D2E GDP 13.3005
38 2HT6 GDP 13.7931
39 5M04 GDP 15.8537
40 3Q72 GNP 16.8675
41 2CJW GDP 18.2927
42 3Q85 GNP 20.7317
43 3EC1 GDP 21.9512
44 3VMF GTP 22.1675
45 6AU6 GDP 22.561
46 3GJ3 GDP 23.1707
47 4HAT GNP 23.1707
48 5UWQ GNP 23.1707
49 5UWU GNP 23.1707
50 3GJ0 GDP 23.1707
51 5UWO GNP 23.1707
52 3GJ7 GDP 23.1707
53 3CH5 GDP 23.1707
54 3GJ4 GDP 23.1707
55 3GJ8 GDP 23.1707
56 5BXQ GDP 23.1707
57 3GJ5 GDP 23.1707
58 1TAD GDP 28.0488
59 1TAD ALF 28.0488
60 6CRK GDP 29.2683
61 4HDO GNP 31.7073
62 5E95 GDP 32.1429
63 6BVJ GNP 32.3353
64 6D5E GNP 32.3353
65 6BVK GNP 32.3353
66 3T1O GDP 32.9268
67 2QN6 GDP 33.3333
68 5JCZ GDP 33.5366
69 3CPJ GDP 35.3659
70 5O74 GDP 42.0732
71 4DCT GDP 45.122
Pocket No.: 2; Query (leader) PDB : 1S9D; Ligand: AFB; 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: 1s9d.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
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