Receptor
PDB id Resolution Class Description Source Keywords
5CK5 2.4 Å NON-ENZYME: SIGNAL_HORMONE SIGNAL RECOGNITION PARTICLE RECEPTOR SRB-GDP-MG FROM CHAETOM THERMOPHILUM CHAETOMIUM THERMOPHILUM ARF-LIKE GTPASE PROTEIN TRANSLOCATION SIGNALING PROTEIN
Ref.: STRUCTURE AND SWITCH CYCLE OF SR BETA AS ANCESTRAL EUKARYOTIC GTPASE ASSOCIATED WITH SECRETORY MEMBRAN STRUCTURE V. 23 1838 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:402;
D:402;
B:402;
C:402;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
GDP D:401;
C:401;
B:401;
A:401;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5CK5 2.4 Å NON-ENZYME: SIGNAL_HORMONE SIGNAL RECOGNITION PARTICLE RECEPTOR SRB-GDP-MG FROM CHAETOM THERMOPHILUM CHAETOMIUM THERMOPHILUM ARF-LIKE GTPASE PROTEIN TRANSLOCATION SIGNALING PROTEIN
Ref.: STRUCTURE AND SWITCH CYCLE OF SR BETA AS ANCESTRAL EUKARYOTIC GTPASE ASSOCIATED WITH SECRETORY MEMBRAN STRUCTURE V. 23 1838 2015
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 286 families.
1 5CK4 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 5CK5 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 209 families.
1 5CK4 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 5CK5 - 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 174 families.
1 5CK4 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 5CK5 - 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
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5CK5; Ligand: GDP; Similar sites found with APoc: 169
This union binding pocket(no: 1) in the query (biounit: 5ck5.bio3) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 4LC1 GDP 2.21519
2 5FG3 GDP 2.21519
3 5W7Q GDP 2.21519
4 3MD0 GDP 2.21519
5 2C78 GNP 2.21519
6 3TK1 GDP 2.21519
7 1RYH GNP 2.46305
8 1WF3 GNP 2.65781
9 1MKY GDP 2.8481
10 1YRB GDP 3.05344
11 3WYA GDP 3.22581
12 2RCN GDP 3.48101
13 3PQC GDP 3.58974
14 1TQ4 GDP 4.43038
15 4NON GDP 4.61538
16 5M04 GDP 4.72222
17 4J0Q GDP 4.74684
18 1Z2A GDP 4.7619
19 6G14 G4P 5.10204
20 5WDR GNP 5.26316
21 1G7S GDP 5.37975
22 3T5G GDP 5.52486
23 2ZEJ GDP 5.97826
24 4RD0 GDP 6.01266
25 4HI0 GDP 6.03015
26 5YT0 GDP 6.32911
27 4B47 GDP 6.64557
28 2CJW GDP 6.77083
29 3CNL GNP 6.87023
30 2GJ8 ALF GDP 6.97674
31 5OEC GDP 7.10383
32 4DKX GDP 7.40741
33 2HT6 GDP 7.47126
34 2QN6 GDP 7.52688
35 3RAB GNP 7.69231
36 1SVI GDP 7.69231
37 2A9K GDP 8.02139
38 1ZJ6 G3D 8.02139
39 1UAD GNP 8.08081
40 2A5J GDP 8.37696
41 5LEF GTP 8.37696
42 3RWO GDP 8.64865
43 3DOE GTP 8.85417
44 5O74 GDP 8.88889
45 4ZI2 GNP 8.94737
46 3NKV GNP 9.14286
47 2FFQ GSP 9.35672
48 3CPJ GDP 9.41704
49 5KUT GDP 9.52381
50 1J2J GTP 9.63855
51 1O3Y GTP 9.63855
52 2J59 GTP 9.63855
53 2BME GNP 9.67742
54 1S9D GDP 9.7561
55 1RE0 GDP 9.7561
56 1KY3 GDP 9.89011
57 4P3Y GDP 10.1266
58 3U6B GDP 10.1266
59 1D8T GDP 10.1266
60 5JBQ GDP 10.1266
61 4G5G GDP 10.1266
62 3U6K GDP 10.1266
63 3BC1 GNP 10.2564
64 1Z0A GDP 10.3448
65 2F9L GDP 10.5528
66 1Z0F GDP 10.6145
67 3TKL GTP 10.7143
68 5XKT GNP 10.7595
69 3Q72 GNP 10.8434
70 3SFV GDP 11.0497
71 5SZH GNP 11.1111
72 1VG0 GDP 11.1111
73 5UWH GNP 11.3924
74 5UWT GNP 11.3924
75 5UWR GNP 11.3924
76 5UWS GNP 11.3924
77 5UWI GNP 11.3924
78 5DHF GNP 11.3924
79 5UWQ GNP 11.3924
80 6CIT GNP 11.3924
81 5UWO GNP 11.3924
82 5UWJ GNP 11.3924
83 5UWU GNP 11.3924
84 5UWP GNP 11.3924
85 5DIF GNP 11.3924
86 5UWW GNP 11.3924
87 1OIX GDP 11.5183
88 1OIV GDP 11.5183
89 1Z08 GNP 11.7647
90 5XC5 GTP 11.9318
91 2EW1 GNP 11.9403
92 3AQ4 GDP 11.9565
93 3GJ8 GDP 12.2172
94 3GJ0 GDP 12.2172
95 3GJ7 GDP 12.2172
96 5JCZ GDP 12.2905
97 3WYF GTP 12.3288
98 1VG9 GDP 12.4324
99 1VG1 GDP 12.4324
100 2W2X GSP 12.4324
101 4HAT GNP 12.5
102 4YLG GDP 12.7168
103 2HV8 GTP 12.7907
104 1TU3 GNP 12.8655
105 1Z0J GTP 12.9412
106 1YVD GNP 13.0178
107 5Z2M GTP 13.0682
108 4HDO GNP 13.1737
109 1GUA GNP 13.1737
110 2D7C GTP 13.1737
111 4HDQ GNP 13.1737
112 3QBT GNP 13.5714
113 2EFE GNH 13.8122
114 4C4P GNP 14.0187
115 1KSH GDP 14.5161
116 3GJ5 GDP 14.7059
117 3WYG GTP 14.8352
118 3GJ3 GDP 15.1515
119 1WA5 GTP 15.3409
120 1Z0K GTP 15.942
121 5HCN GCP 16.4751
122 4M9Q GNP 17.1806
123 5BXQ GDP 17.3228
124 3MJH GTP 17.6471
125 2G77 GDP 17.6768
126 2C5L GTP 17.9191
127 1ZD9 GDP 18.0851
128 1UPT GTP 18.1287
129 5E95 GDP 18.4524
130 6BVJ GNP 18.5629
131 6D59 GNP 18.5629
132 6BVL GNP 18.5629
133 6BVI GNP 18.5629
134 6BVK GNP 18.5629
135 6D5L GNP 18.5629
136 6D56 GNP 18.5629
137 6D5E GNP 18.5629
138 6D5J GNP 18.5629
139 6D5H GNP 18.5629
140 6D55 GNP 18.5629
141 6D5V GNP 18.5629
142 6D5G GNP 18.5629
143 1WQ1 GDP 18.6747
144 3DDC GNP 18.6747
145 1CLU DBG 18.6747
146 3KUD GDP 18.6747
147 1F6B GDP 18.6869
148 2HCJ GDP 18.9189
149 1D5C GDP 19.1358
150 2QTV GNP 19.1617
151 5OCG GNP 19.5767
152 5TAR GDP 20
153 5TB5 GDP 20
154 2X77 GDP 20.1058
155 4V0K GDP 20.1183
156 5O2T GSP 20.7101
157 5WLB GNP 21.0843
158 1Z06 GNP 21.164
159 4ZKD GDP 21.8354
160 3Q85 GNP 21.8935
161 1LFD GNP 24.1379
162 3GJ4 GDP 24.2424
163 5EE5 GTP 31.5789
164 2A5F GTP 32
165 1R4A GNP 32.1212
166 3PCR GTP 33.3333
167 1YZG GDP 33.5196
168 2W83 GTP 33.9394
169 3N5C GDP 34.5679
Pocket No.: 2; Query (leader) PDB : 5CK5; Ligand: GDP; 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: 5ck5.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5CK5; Ligand: GDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5ck5.bio2) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5CK5; Ligand: GDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5ck5.bio4) has 15 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback