Receptor
PDB id Resolution Class Description Source Keywords
2CNW 2.39 Å NON-ENZYME: SIGNAL_HORMONE GDPALF4 COMPLEX OF THE SRP GTPASES FFH AND FTSY THERMUS AQUATICUS INNER MEMBRANE MEMBRANE TARGETING NUCLEOTIDE-BINDING GDP- ALUMINUM FLUORIDE SIGNAL RECOGNITION PARTICLE RNA-BINDING GTP-BINDING CELL DIVISION SIGNAL SEQUENCE RECOGNITION SRP FFH FTSY GTPASE MEMBRANE CELL CYCLE CELL DIVISION/COMPLEX SIGNAL RECOGNITION
Ref.: STRUCTURE OF A GDP:ALF(4) COMPLEX OF THE SRP GTPASES FFH AND FTSY, AND IDENTIFICATION OF A PERIPHERAL NUCLEOTIDE INTERACTION SITE. J.MOL.BIOL. V. 360 631 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5GP D:3001;
E:3001;
F:3001;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
363.221 C10 H14 N5 O8 P c1nc2...
GDP ALF A:1001;
B:1001;
C:1001;
D:1001;
E:1001;
F:1001;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
submit data
543.152 n/a [P+](...
MG A:1002;
B:1002;
C:1002;
D:1002;
E:1002;
F:1002;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1RJ9 1.9 Å NON-ENZYME: SIGNAL_HORMONE STRUCTURE OF THE HETERODIMER OF THE CONSERVED GTPASE DOMAINS SIGNAL RECOGNITION PARTICLE (FFH) AND ITS RECEPTOR (FTSY) THERMUS AQUATICUS SRP-GTPASE DOMAIN HETERODIMER NUCLEOTIDE TWINNING PROTEINCOMPLEX PROTEIN TRANSPORT
Ref.: SUBSTRATE TWINNING ACTIVATES THE SIGNAL RECOGNITION PARTICLE AND ITS RECEPTOR NATURE V. 427 215 2004
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 263 families.
1 1OKK - GCP C11 H18 N5 O13 P3 c1nc2c(n1[....
2 2J7P - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
3 2CNW - GDP ALF n/a n/a
4 1RJ9 - GCP C11 H18 N5 O13 P3 c1nc2c(n1[....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 196 families.
1 1OKK - GCP C11 H18 N5 O13 P3 c1nc2c(n1[....
2 2J7P - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
3 2CNW - GDP ALF n/a n/a
4 1RJ9 - GCP C11 H18 N5 O13 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 171 families.
1 1OKK - GCP C11 H18 N5 O13 P3 c1nc2c(n1[....
2 2J7P - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
3 2CNW - GDP ALF n/a n/a
4 1RJ9 - GCP C11 H18 N5 O13 P3 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5GP; Similar ligands found: 156
No: Ligand ECFP6 Tc MDL keys Tc
1 5GP 1 1
2 G 1 1
3 GDP 0.828947 0.986486
4 GP3 0.815789 0.960526
5 GP2 0.805195 0.948052
6 GTP 0.797468 0.986486
7 GNH 0.794872 0.973333
8 G2P 0.777778 0.948052
9 GMV 0.775 0.960526
10 GCP 0.765432 0.960526
11 G1R 0.765432 0.973333
12 GDP MG 0.7625 0.935065
13 GAV 0.759036 0.948052
14 GSP 0.756098 0.935897
15 GNP 0.756098 0.960526
16 GDP BEF 0.753086 0.911392
17 ALF 5GP 0.753086 0.9
18 GMP 0.732394 0.866667
19 GTP MG 0.72619 0.935065
20 BEF GDP 0.72619 0.9
21 GPG 0.724138 0.948052
22 GCP G 0.717647 0.947368
23 G2R 0.712644 0.948052
24 GDP AF3 0.701149 0.9
25 GDP ALF 0.701149 0.9
26 Y9Z 0.692308 0.890244
27 GDC 0.692308 0.948052
28 GKE 0.692308 0.948052
29 GDD 0.692308 0.948052
30 YGP 0.681319 0.9125
31 G G 0.677778 0.947368
32 G3A 0.677419 0.960526
33 G5P 0.670213 0.960526
34 GFB 0.666667 0.948052
35 GDR 0.666667 0.948052
36 GTG 0.666667 0.924051
37 6CK 0.659574 0.924051
38 3GP 0.65 0.959459
39 GKD 0.645833 0.948052
40 JB2 0.645833 0.948052
41 GPD 0.639175 0.9125
42 GDX 0.639175 0.960526
43 GDP 7MG 0.635417 0.923077
44 G3D 0.617977 0.972973
45 U2G 0.617647 0.924051
46 IMP 0.609756 0.972603
47 2GP 0.609756 0.946667
48 JB3 0.607843 0.935897
49 CG2 0.605769 0.924051
50 G4P 0.604396 0.972973
51 DGP 0.60241 0.922078
52 DG 0.60241 0.922078
53 FEG 0.601942 0.890244
54 NGD 0.601942 0.948052
55 ZGP 0.596154 0.879518
56 0O2 0.595745 0.972973
57 2MD 0.584906 0.879518
58 G7M 0.583333 0.960526
59 CAG 0.583333 0.869048
60 G A A A 0.579439 0.935065
61 U A G G 0.574074 0.947368
62 MGD 0.568807 0.879518
63 DBG 0.566372 0.935897
64 PGD 0.5625 0.9125
65 MD1 0.5625 0.879518
66 P2G 0.55814 0.894737
67 FE9 0.553571 0.784946
68 I2C FE2 CMO CMO 0.54955 0.818182
69 P1G 0.545455 0.883117
70 GH3 0.542553 0.96
71 TPG 0.53913 0.829545
72 GPX 0.53125 0.933333
73 DGI 0.527473 0.910256
74 G1R G1R 0.525862 0.911392
75 PGD O 0.521368 0.83908
76 DGT 0.521277 0.910256
77 G4M 0.520325 0.869048
78 G G U 0.519231 0.947368
79 G C 0.513514 0.911392
80 93A 0.511364 0.821429
81 IDP 0.505495 0.959459
82 MGQ 0.505155 0.948052
83 C2R 0.5 0.893333
84 BGO 0.5 0.911392
85 AMP 0.5 0.905405
86 AMZ 0.5 0.905405
87 A 0.5 0.905405
88 AIR 0.493671 0.890411
89 MGV 0.49 0.901235
90 SGP 0.488889 0.8375
91 U G A 0.488189 0.9
92 NIA 0.488095 0.8375
93 GPC 0.474138 0.890244
94 G G G RPC 0.473684 0.886076
95 GGM 0.473684 0.888889
96 71V 0.47191 0.85
97 APC G U 0.470085 0.897436
98 MGP 0.46875 0.948052
99 C2E 0.468085 0.933333
100 35G 0.468085 0.945946
101 PCG 0.468085 0.945946
102 G1G 0.466102 0.9125
103 7RA 0.465909 0.918919
104 AAM 0.465909 0.905405
105 RMB 0.465909 0.813333
106 FAI 0.465909 0.905405
107 1RB 0.465116 0.824324
108 6G0 0.463918 0.948052
109 5GP 5GP 0.463158 0.894737
110 G G G C 0.462185 0.924051
111 RBZ 0.45977 0.815789
112 UCG 0.459016 0.923077
113 A G C C 0.458333 0.923077
114 DG DG 0.456311 0.876543
115 G U34 0.45614 0.9
116 IMO 0.449438 0.866667
117 A G U 0.446154 0.9
118 G C C C 0.443548 0.935897
119 IRN 0.443038 0.808219
120 PMO 0.43956 0.792208
121 7RP 0.438202 0.864865
122 GTA 0.436364 0.924051
123 P2P 0.433333 0.842105
124 JLN 0.433333 0.88
125 XMP 0.428571 0.907895
126 PGS 0.425532 0.804878
127 RVP 0.423529 0.84
128 G2Q 0.423077 0.948052
129 ADP 0.419355 0.906667
130 A2D 0.417582 0.881579
131 ABM 0.417582 0.857143
132 GUO 0.415842 0.932432
133 CA0 0.410526 0.883117
134 2SA 0.41 0.871795
135 1YD 0.409091 0.933333
136 4BW 0.409091 0.933333
137 AP2 0.408602 0.871795
138 A12 0.408602 0.871795
139 BA3 0.408602 0.881579
140 6C6 0.408163 0.825
141 25A 0.407767 0.906667
142 NOS 0.406977 0.813333
143 AMP MG 0.406593 0.833333
144 ATP 0.40625 0.906667
145 AP5 0.404255 0.881579
146 B4P 0.404255 0.881579
147 6IA 0.40404 0.785714
148 ACQ 0.40404 0.883117
149 ANP 0.40404 0.883117
150 CGP 0.403361 0.878049
151 3ZE 0.402062 0.871795
152 APC 0.402062 0.871795
153 5FA 0.402062 0.906667
154 AQP 0.402062 0.906667
155 N6P 0.4 0.853333
156 AN2 0.4 0.894737
Ligand no: 2; Ligand: GDP ALF; Similar ligands found: 110
No: Ligand ECFP6 Tc MDL keys Tc
1 GDP ALF 1 1
2 ALF 5GP 0.857143 1
3 GTP MG 0.806818 0.91358
4 GDP MG 0.802326 0.91358
5 GDP AF3 0.8 1
6 GDP BEF 0.793103 0.938272
7 BEF GDP 0.786517 0.950617
8 GDP 7MG 0.71 0.879518
9 5GP 0.701149 0.9
10 G 0.701149 0.9
11 GDP 0.7 0.888889
12 GP3 0.688889 0.86747
13 GNH 0.673913 0.878049
14 GCP G 0.666667 0.901235
15 G G 0.666667 0.901235
16 GP2 0.663043 0.857143
17 GTP 0.659574 0.888889
18 G1R 0.652632 0.878049
19 GCP 0.652632 0.86747
20 G2P 0.645833 0.857143
21 GSP 0.645833 0.847059
22 GNP 0.645833 0.86747
23 GMV 0.642105 0.890244
24 GAV 0.632653 0.857143
25 G2R 0.613861 0.857143
26 GMP 0.593023 0.802469
27 GPG 0.592233 0.857143
28 G1R G1R 0.591667 0.869048
29 6CK 0.588785 0.903614
30 PGD O 0.586777 0.784946
31 Y9Z 0.584906 0.808989
32 GDC 0.584906 0.857143
33 GDD 0.584906 0.857143
34 GKE 0.584906 0.857143
35 GTG 0.579439 0.858824
36 GFB 0.579439 0.857143
37 GDR 0.579439 0.857143
38 I2C FE2 CMO CMO 0.576271 0.804348
39 YGP 0.575472 0.827586
40 G3A 0.574074 0.86747
41 G5P 0.568807 0.86747
42 ADP ALF 0.565657 0.9125
43 ALF ADP 0.565657 0.9125
44 JB2 0.563636 0.857143
45 GKD 0.563636 0.857143
46 U A G G 0.559322 0.901235
47 GDX 0.558559 0.86747
48 GPD 0.558559 0.827586
49 G A A A 0.550847 0.890244
50 G3D 0.54902 0.876543
51 FEG 0.543103 0.808989
52 G4P 0.538462 0.876543
53 ZGP 0.538462 0.8
54 3GP 0.536842 0.864198
55 JB3 0.534483 0.847059
56 NGD 0.529915 0.879518
57 0O2 0.518519 0.876543
58 U2G 0.516949 0.837209
59 2MD 0.516667 0.8
60 CAG 0.516393 0.811111
61 G G U 0.508772 0.878049
62 CG2 0.508333 0.837209
63 G C 0.504132 0.869048
64 MGD 0.504065 0.8
65 MD1 0.5 0.8
66 DBG 0.492188 0.847059
67 2GP 0.489796 0.853659
68 PGD 0.488189 0.827586
69 U G A 0.481752 0.858824
70 TPG 0.48062 0.757895
71 FE9 0.480315 0.755102
72 GPX 0.477064 0.841463
73 DGI 0.471154 0.823529
74 G G G C 0.46875 0.858824
75 G G G RPC 0.467742 0.845238
76 A G C C 0.465116 0.879518
77 GH3 0.458716 0.865854
78 G4M 0.456522 0.791209
79 DG 0.455446 0.833333
80 DGP 0.455446 0.833333
81 BGO 0.455285 0.825581
82 DGT 0.453704 0.823529
83 APC G U 0.453125 0.855422
84 DG DG 0.451327 0.837209
85 G C C C 0.451128 0.869048
86 P2G 0.45098 0.807229
87 P1G 0.442308 0.797619
88 ADP PO3 0.438095 0.8375
89 IDP 0.438095 0.864198
90 ATP MG 0.433962 0.829268
91 GGM 0.433071 0.806818
92 A G U 0.432624 0.858824
93 IMP 0.431373 0.875
94 AF3 ADP 3PG 0.430894 0.902439
95 G1G 0.427481 0.848837
96 ADP MG 0.423077 0.829268
97 ADP BEF 0.419048 0.853659
98 BEF ADP 0.419048 0.853659
99 ADP VO4 0.418182 0.829268
100 VO4 ADP 0.418182 0.829268
101 G U34 0.417323 0.858824
102 5GP 5GP 0.416667 0.851852
103 ALF GDP 0.414414 0.936709
104 G7M 0.413462 0.890244
105 GPC 0.412214 0.872093
106 SGP 0.409524 0.758621
107 C2E 0.407407 0.841463
108 PCG 0.407407 0.851852
109 35G 0.407407 0.851852
110 OMC OMU OMG OMG U 0.406897 0.83908
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1RJ9; Ligand: GCP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 1rj9.bio1) has 55 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1RJ9; Ligand: GCP; Similar sites found: 121
This union binding pocket(no: 2) in the query (biounit: 1rj9.bio1) has 69 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1Z6T ADP 0.0002519 0.50055 2.63158
2 1G6O ADP 0.00002942 0.55746 2.66667
3 1TQ4 GDP 0.000009055 0.5576 3.28947
4 5VGR GDP 0.001605 0.46205 3.33333
5 1KA1 A3P 0.02311 0.41278 3.33333
6 4LO2 GAL BGC 0.04466 0.4046 3.37838
7 4R43 GDP 0.0008707 0.49445 4
8 1YTM ATP 0.001062 0.46239 4
9 1AZT GSP 0.00007868 0.40455 4
10 3PQC GDP 0.00009038 0.53315 4.10256
11 2NCD ADP 0.00007241 0.5702 4.27632
12 1SQ5 ADP 0.0002196 0.51961 4.54545
13 3BER AMP 0.003229 0.46473 4.81928
14 1VG8 GNP 0.00004666 0.4001 4.83092
15 2ZFI ADP 0.0002794 0.5202 5
16 1JQN DCO 0.01628 0.42408 5
17 3CV2 OXL 0.03789 0.42367 5
18 2WIC GNP 0.000004129 0.60761 5.24345
19 4P4T GDP 0.000007339 0.56777 5.26316
20 1TAD ALF 0.00007594 0.40447 5.26316
21 1TAD GDP 0.00007594 0.40447 5.26316
22 5H68 AGS 0.005287 0.40524 5.33333
23 1G7S GDP 0.00002266 0.56991 5.59211
24 1IWE IMP 0.0005134 0.45205 5.66667
25 4OHY ANP 0.0003789 0.47082 5.92105
26 1CS4 GSP 0.00009703 0.4845 6.22222
27 2BEK ATP 0.002646 0.40315 6.22568
28 1ZD9 GDP 0.00001225 0.55733 6.38298
29 4QOS ADP 0.0002401 0.51197 6.41509
30 4V0K GDP 0.00005734 0.50653 6.50888
31 2CBZ ATP 0.000003944 0.65442 6.75105
32 3U6B GDP 0.000002139 0.63953 6.85279
33 2BVN GNP 0.000003249 0.59789 6.87023
34 5HCN GCP 0.000000749 0.40072 6.89655
35 1GOJ ADP 0.00001474 0.61548 6.90789
36 1UPT GTP 0.000004117 0.40487 7.01754
37 1FQJ GDP 0.00005043 0.51353 7.14286
38 1FQJ ALF 0.02917 0.42482 7.14286
39 2DPY ADP 0.0001057 0.55636 7.23684
40 5IRR GSP 0.00007212 0.51129 7.23684
41 2ZTS ADP 0.00214 0.45214 7.23684
42 2FNA ADP 0.0004522 0.47529 7.33333
43 4BQS ADP 0.00003347 0.56828 7.38636
44 3BFX A3P 0.005367 0.43337 7.77027
45 1W7J ADP BEF 0.001979 0.4577 7.89474
46 1QF5 GDP 0.00005146 0.45749 7.89474
47 5FTB ANP 0.00009406 0.53228 8
48 5FHD ADP ALF 0.0002717 0.48963 8
49 3NHB ADP 0.0001442 0.5539 8.22368
50 3T34 GDP 0.00009453 0.50144 8.33333
51 1U4J MAN 0.04928 0.40637 8.47458
52 4BAS GNP 0.00001063 0.40244 8.54271
53 2G77 GDP 0.00002608 0.54768 8.55263
54 2G77 AF3 0.03582 0.41989 8.55263
55 4AG5 ADP 0.00001511 0.60778 8.66667
56 3EZ2 ADP 0.0004168 0.51723 8.66667
57 1GXU 2HP 0.00009542 0.55472 8.79121
58 4IEE AGS 0.0002509 0.52901 9
59 2WJG GDP 0.00001999 0.57996 9.04255
60 1JI0 ATP 0.000102 0.55722 9.16667
61 1YZN GNP 0.00007905 0.49212 9.18919
62 3K7S R52 0.02538 0.41777 9.49721
63 4A7W GTP 0.04449 0.41074 9.53947
64 2VOH CIT 0.04287 0.42567 9.55414
65 4DKX GDP 0.000003196 0.62149 9.72222
66 2ODE ALF GDP 0.0001011 0.40203 9.92908
67 4M9Q GNP 0.00001296 0.54494 10.1322
68 3T12 GDP ALF 0.00006819 0.51239 10.6061
69 2WKQ GTP 0.0002378 0.48368 10.8553
70 5DI3 GNP 0.00001567 0.54122 11.3514
71 5BQ5 ADP BEF 0.0002875 0.50808 11.6402
72 3GJ8 GDP 0.000004174 0.60737 11.7647
73 1L2T ATP 0.004514 0.42394 11.9149
74 4J0Q GDP 0.000002306 0.63779 12
75 4NEC SAH 0.03221 0.40237 12.1212
76 3GJ0 GDP 0.000003879 0.6171 12.2172
77 2Y8E GNP 0.00009088 0.49362 12.2905
78 1GUA GNP 0.0001372 0.48205 12.3457
79 2CK3 ANP 0.00108 0.46608 12.8289
80 2CK3 ADP 0.001042 0.45524 12.8289
81 4NON GDP 0.0005906 0.45207 12.8289
82 3FKQ ATP 0.0003221 0.49544 12.8686
83 5J1J ANP 0.0000178 0.40151 13.6842
84 1WQ1 GDP 0.00009156 0.50205 13.8554
85 1WQ1 AF3 0.02677 0.4284 13.8554
86 5UFQ GNP 0.00002632 0.40232 13.8554
87 5UWQ GNP 0.0001173 0.48491 13.9241
88 5UWJ GNP 0.0001392 0.48178 13.9241
89 5JCP GDP ALF 0.0001079 0.51816 14.3333
90 4H1V GNP 0.00004251 0.53752 15
91 1WA5 GTP 0.0002418 0.45804 15.3409
92 1YRB GDP 0.000001316 0.4007 15.6489
93 4CVN ADP 0.00001086 0.61047 16.0584
94 2A5J GDP 0.000008659 0.58396 16.2304
95 2GJ8 ALF GDP 0.000033 0.50807 16.2791
96 2HF9 GSP 0.00006511 0.52866 16.3717
97 1XEX ATP 0.001664 0.43959 16.4835
98 4WZA ACP 0.001494 0.41491 17
99 4WZA ADP 0.001543 0.41441 17
100 1S9D GDP 0.000003197 0.61328 17.6829
101 1GP2 GDP 0.0001835 0.48867 18.3099
102 3N5C GDP 0.0000009495 0.64898 18.5185
103 3PCR GTP 0.00004192 0.51709 19.1358
104 5EE5 GTP 0.000005879 0.40605 19.883
105 1R4A GNP 0.000009579 0.40995 21.2121
106 5TAR GDP 0.00001681 0.56302 22.1622
107 1WDT GTP 0.00001183 0.55804 22.3684
108 3LXR GDP 0.0001153 0.52788 23.2432
109 4LC1 GDP 0.000001354 0.64094 23.6842
110 1M2O GNP 0.00003009 0.40155 24.2105
111 1TX4 ALF GDP 0.0004309 0.47223 24.2938
112 1J2J GTP 0.00003386 0.5212 24.4444
113 1QHH ATP 0.00454 0.45249 24.5509
114 4HI0 GDP 0.00002288 0.53908 24.6231
115 3MJH GTP 0.0001143 0.48936 26.7857
116 3QBT GNP 0.00006423 0.50006 27.5862
117 4LHW GNP 0.0001156 0.48914 27.5862
118 1Z2A GDP 0.0001512 0.4924 33.3333
119 1Z0J GTP 0.00005409 0.49905 33.8983
120 2BCG GDP 0.00004726 0.52983 35.9223
121 2OM2 GDP 0.00008879 0.51199 41.6667
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