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(=O)...
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 289 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 214 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 181 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 (2D)
Ligand no: 1; Ligand: 5GP; Similar ligands found: 159
No: Ligand ECFP6 Tc MDL keys Tc
1 G 1 1
2 5GP 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 GAV 0.759036 0.948052
13 GSP 0.756098 0.935897
14 GNP 0.756098 0.960526
15 9GM 0.756098 0.960526
16 ALF 5GP 0.753086 0.9
17 GDP BEF 0.743902 0.947368
18 GTP MG 0.73494 0.972973
19 GMP 0.732394 0.866667
20 GPG 0.724138 0.948052
21 G2R 0.712644 0.948052
22 GDP ALF 0.701149 0.9
23 GDP AF3 0.701149 0.9
24 GKE 0.692308 0.948052
25 GDC 0.692308 0.948052
26 Y9Z 0.692308 0.890244
27 GDD 0.692308 0.948052
28 YGP 0.681319 0.9125
29 G3A 0.677419 0.960526
30 G5P 0.670213 0.960526
31 KB7 0.666667 0.8375
32 GFB 0.666667 0.948052
33 GDR 0.666667 0.948052
34 GTG 0.666667 0.924051
35 6CK 0.659574 0.924051
36 3GP 0.65 0.959459
37 JB2 0.645833 0.948052
38 GKD 0.645833 0.948052
39 GDX 0.639175 0.960526
40 GPD 0.639175 0.9125
41 GDP 7MG 0.635417 0.923077
42 G3D 0.617977 0.972973
43 U2G 0.617647 0.924051
44 KBD 0.612903 0.8375
45 2GP 0.609756 0.946667
46 IMP 0.609756 0.972603
47 JB3 0.607843 0.935897
48 CG2 0.605769 0.924051
49 G4P 0.604396 0.972973
50 DG 0.60241 0.922078
51 DGP 0.60241 0.922078
52 NGD 0.601942 0.948052
53 FEG 0.601942 0.890244
54 ZGP 0.596154 0.879518
55 0O2 0.595745 0.972973
56 KBJ 0.587629 0.807229
57 2MD 0.584906 0.879518
58 G7M 0.583333 0.960526
59 CAG 0.583333 0.869048
60 MGD 0.568807 0.879518
61 DBG 0.566372 0.935897
62 MD1 0.5625 0.879518
63 PGD 0.5625 0.9125
64 P2G 0.55814 0.894737
65 FE9 0.553571 0.784946
66 P1G 0.545455 0.883117
67 GH3 0.542553 0.96
68 I2C FE2 CMO CMO 0.539823 0.818182
69 TPG 0.53913 0.829545
70 GPX 0.53125 0.933333
71 DGI 0.527473 0.910256
72 G1R G1R 0.525862 0.911392
73 PGD O 0.521368 0.83908
74 DGT 0.521277 0.910256
75 G4M 0.520325 0.869048
76 AKW 0.513761 0.878049
77 G C 0.513514 0.911392
78 93A 0.511364 0.821429
79 IDP 0.505495 0.959459
80 MGQ 0.505155 0.948052
81 C2R 0.5 0.893333
82 A 0.5 0.905405
83 BGO 0.5 0.911392
84 AMZ 0.5 0.905405
85 AMP 0.5 0.905405
86 AIR 0.493671 0.890411
87 MGV 0.49 0.901235
88 QBQ 0.489362 0.972973
89 SGP 0.488889 0.8375
90 NIA 0.488095 0.8375
91 GPC 0.474138 0.890244
92 GGM 0.473684 0.888889
93 71V 0.47191 0.85
94 R5I 0.46875 0.933333
95 MGP 0.46875 0.948052
96 R7I 0.46875 0.933333
97 C2E 0.468085 0.933333
98 PCG 0.468085 0.945946
99 35G 0.468085 0.945946
100 G1G 0.466102 0.9125
101 7RA 0.465909 0.918919
102 FAI 0.465909 0.905405
103 AAM 0.465909 0.905405
104 RMB 0.465909 0.813333
105 1RB 0.465116 0.824324
106 6G0 0.463918 0.948052
107 5GP 5GP 0.463158 0.894737
108 RBZ 0.45977 0.815789
109 UCG 0.459016 0.923077
110 APC G U 0.458333 0.897436
111 IMO 0.449438 0.866667
112 6MZ 0.444444 0.868421
113 IRN 0.443038 0.808219
114 PMO 0.43956 0.792208
115 7RP 0.438202 0.864865
116 NYZ 0.4375 0.923077
117 GTA 0.436364 0.924051
118 JLN 0.433333 0.88
119 P2P 0.433333 0.842105
120 CZF 0.43299 0.92
121 XMP 0.428571 0.907895
122 M7G A2M G 0.427586 0.818182
123 PGS 0.425532 0.804878
124 RVP 0.423529 0.84
125 G2Q 0.423077 0.948052
126 ADP 0.419355 0.906667
127 ABM 0.417582 0.857143
128 45A 0.417582 0.857143
129 A2D 0.417582 0.881579
130 PRT 0.416667 0.945946
131 GUO 0.415842 0.932432
132 AT4 0.414894 0.871795
133 AMP MG 0.411111 0.866667
134 CA0 0.410526 0.883117
135 2SA 0.41 0.871795
136 OK8 0.41 0.87013
137 1YD 0.409091 0.933333
138 4BW 0.409091 0.933333
139 BA3 0.408602 0.881579
140 AP2 0.408602 0.871795
141 A12 0.408602 0.871795
142 6C6 0.408163 0.825
143 25A 0.407767 0.906667
144 NOS 0.406977 0.813333
145 ATP 0.40625 0.906667
146 KG4 0.40625 0.883117
147 HEJ 0.40625 0.906667
148 B4P 0.404255 0.881579
149 AP5 0.404255 0.881579
150 6IA 0.40404 0.785714
151 ACQ 0.40404 0.883117
152 ANP 0.40404 0.883117
153 CGP 0.403361 0.878049
154 3ZE 0.402062 0.871795
155 5FA 0.402062 0.906667
156 APC 0.402062 0.871795
157 AQP 0.402062 0.906667
158 AN2 0.4 0.894737
159 N6P 0.4 0.853333
Ligand no: 2; Ligand: GDP ALF; Similar ligands found: 102
No: Ligand ECFP6 Tc MDL keys Tc
1 GDP ALF 1 1
2 ALF 5GP 0.857143 1
3 GDP BEF 0.825581 0.925
4 GTP MG 0.816092 0.924051
5 GDP AF3 0.8 1
6 GDP 7MG 0.71 0.879518
7 5GP 0.701149 0.9
8 G 0.701149 0.9
9 GDP 0.7 0.888889
10 GP3 0.688889 0.86747
11 GNH 0.673913 0.878049
12 GP2 0.663043 0.857143
13 GTP 0.659574 0.888889
14 G1R 0.652632 0.878049
15 GCP 0.652632 0.86747
16 GSP 0.645833 0.847059
17 9GM 0.645833 0.86747
18 GNP 0.645833 0.86747
19 G2P 0.645833 0.857143
20 GMV 0.642105 0.890244
21 GAV 0.632653 0.857143
22 G2R 0.613861 0.857143
23 GMP 0.593023 0.802469
24 GPG 0.592233 0.857143
25 G1R G1R 0.591667 0.869048
26 6CK 0.588785 0.903614
27 PGD O 0.586777 0.784946
28 GDC 0.584906 0.857143
29 GDD 0.584906 0.857143
30 Y9Z 0.584906 0.808989
31 GKE 0.584906 0.857143
32 GDR 0.579439 0.857143
33 GFB 0.579439 0.857143
34 GTG 0.579439 0.858824
35 YGP 0.575472 0.827586
36 G3A 0.574074 0.86747
37 KB7 0.571429 0.77907
38 G5P 0.568807 0.86747
39 ALF ADP 0.565657 0.9125
40 GKD 0.563636 0.857143
41 JB2 0.563636 0.857143
42 GDX 0.558559 0.86747
43 GPD 0.558559 0.827586
44 I2C FE2 CMO CMO 0.553719 0.804348
45 G3D 0.54902 0.876543
46 FEG 0.543103 0.808989
47 G4P 0.538462 0.876543
48 ZGP 0.538462 0.8
49 3GP 0.536842 0.864198
50 JB3 0.534483 0.847059
51 NGD 0.529915 0.879518
52 KBD 0.518519 0.77907
53 0O2 0.518519 0.876543
54 U2G 0.516949 0.837209
55 2MD 0.516667 0.8
56 CAG 0.516393 0.811111
57 CG2 0.508333 0.837209
58 G C 0.504132 0.869048
59 MGD 0.504065 0.8
60 KBJ 0.5 0.752809
61 MD1 0.5 0.8
62 DBG 0.492188 0.847059
63 2GP 0.489796 0.853659
64 PGD 0.488189 0.827586
65 TPG 0.48062 0.757895
66 FE9 0.480315 0.755102
67 GPX 0.477064 0.841463
68 M7G A2M G 0.473333 0.784946
69 DGI 0.471154 0.823529
70 BEF ADP 0.461538 0.839506
71 GH3 0.458716 0.865854
72 G4M 0.456522 0.791209
73 DGP 0.455446 0.833333
74 DG 0.455446 0.833333
75 BGO 0.455285 0.825581
76 APC G U 0.453846 0.855422
77 DGT 0.453704 0.823529
78 P2G 0.45098 0.807229
79 AKW 0.443548 0.818182
80 P1G 0.442308 0.797619
81 ATP MG 0.438095 0.8375
82 IDP 0.438095 0.864198
83 ADP PO3 0.438095 0.8375
84 VO4 ADP 0.435185 0.841463
85 GGM 0.433071 0.806818
86 IMP 0.431373 0.875
87 AF3 ADP 3PG 0.430894 0.902439
88 G1G 0.427481 0.848837
89 ADP BEF 0.427184 0.8375
90 ADP MG 0.427184 0.8375
91 5GP 5GP 0.416667 0.851852
92 ALF GDP 0.415929 0.936709
93 G7M 0.413462 0.890244
94 QBQ 0.412844 0.876543
95 GPC 0.412214 0.872093
96 SGP 0.409524 0.758621
97 R5I 0.409091 0.841463
98 R7I 0.409091 0.841463
99 C2E 0.407407 0.841463
100 PCG 0.407407 0.851852
101 35G 0.407407 0.851852
102 OMC OMU OMG OMG U 0.406897 0.83908
Similar Ligands (3D)
Ligand no: 1; Ligand: 5GP; Similar ligands found: 181
No: Ligand Similarity coefficient
1 IMU 0.9908
2 EO7 0.9905
3 IRP 0.9761
4 LMS 0.9705
5 6CG 0.9705
6 FMP 0.9702
7 8GM 0.9670
8 6OG 0.9662
9 8BR 0.9643
10 SRA 0.9642
11 D5M 0.9581
12 8OP 0.9576
13 DI 0.9557
14 DA 0.9551
15 CMP 0.9481
16 5HM 0.9474
17 6SW 0.9448
18 AS 0.9446
19 8OG 0.9444
20 AOC 0.9444
21 6MA 0.9412
22 ZAS 0.9407
23 5BU 0.9398
24 PFU 0.9366
25 NEC 0.9346
26 7CH 0.9345
27 3DH 0.9341
28 A3N 0.9335
29 FNU 0.9328
30 N5O 0.9319
31 CNU 0.9319
32 BRU 0.9319
33 5AS 0.9308
34 5CM 0.9294
35 NCN 0.9288
36 TMP 0.9283
37 NYM 0.9281
38 QBT 0.9281
39 6SZ 0.9279
40 TKW 0.9278
41 Z8B 0.9277
42 5FU 0.9270
43 UFP 0.9262
44 M2T 0.9253
45 NMN 0.9252
46 U5P 0.9224
47 MTA 0.9223
48 SP1 0.9219
49 7D5 0.9218
50 6SX 0.9214
51 6RE 0.9211
52 J7C 0.9211
53 5IU 0.9207
54 MZP 0.9174
55 4X2 0.9152
56 NWQ 0.9140
57 5HU 0.9140
58 9L3 0.9138
59 C 0.9123
60 2DT 0.9120
61 D4M 0.9119
62 BMQ 0.9115
63 BMP 0.9108
64 EP4 0.9107
65 MCF 0.9100
66 UP6 0.9063
67 RP1 0.9062
68 6J7 0.9056
69 BVP 0.9055
70 DSH 0.9040
71 C5P 0.9030
72 O8M 0.9029
73 PRX 0.9015
74 UMP 0.9002
75 DC 0.8991
76 GJV 0.8990
77 DCM 0.8989
78 DU 0.8989
79 U 0.8986
80 NWZ 0.8980
81 H2U 0.8974
82 3F5 0.8969
83 SSI 0.8968
84 MTE 0.8960
85 NUP 0.8946
86 UMC 0.8941
87 GDP MG 0.8932
88 T3S 0.8920
89 S5P 0.8919
90 ICR 0.8905
91 FN5 0.8895
92 CH 0.8895
93 581 0.8894
94 U6M 0.8893
95 PSU 0.8871
96 16B 0.8861
97 M7G 0.8859
98 O02 0.8851
99 2FA 0.8850
100 CAR 0.8849
101 O7E 0.8845
102 DDN 0.8844
103 G5A 0.8843
104 A8M 0.8839
105 ADP MG 0.8838
106 6CN 0.8830
107 DUS 0.8828
108 A3P 0.8826
109 OMP 0.8819
110 M33 0.8818
111 AD3 0.8816
112 ATM 0.8807
113 JW5 0.8806
114 43J 0.8797
115 T7O 0.8794
116 6AU 0.8793
117 GNG 0.8784
118 ADN 0.8778
119 N8M 0.8776
120 7DD 0.8775
121 U4S 0.8771
122 GAP 0.8768
123 6AD 0.8762
124 ADX 0.8760
125 A4D 0.8759
126 5CD 0.8759
127 1BJ 0.8754
128 A2P 0.8752
129 S4M 0.8752
130 43H 0.8741
131 IXF 0.8739
132 SON 0.8729
133 DOC 0.8728
134 FMC 0.8728
135 DBM 0.8718
136 5YA 0.8713
137 NOC 0.8713
138 ARJ 0.8713
139 NWW 0.8700
140 U2S 0.8699
141 FKJ 0.8695
142 IY5 0.8695
143 13A 0.8685
144 5N5 0.8683
145 AU1 0.8679
146 DAT 0.8677
147 Y3J 0.8666
148 CL9 0.8665
149 IMH 0.8665
150 CC2 0.8659
151 UA2 0.8658
152 MG7 0.8657
153 2OM 0.8656
154 U3S 0.8655
155 U1S 0.8655
156 100 0.8648
157 M7M 0.8647
158 ECZ 0.8641
159 2ZI 0.8639
160 5FD 0.8639
161 O7M 0.8636
162 PNJ 0.8629
163 TBN 0.8621
164 RFZ 0.8610
165 3AD 0.8609
166 GLC G6P 0.8606
167 IXE 0.8598
168 5CJ 0.8596
169 M0Y 0.8587
170 LRT 0.8587
171 DN8 0.8586
172 824 0.8575
173 0NH 0.8561
174 IYX 0.8555
175 A5A 0.8547
176 9W8 0.8546
177 TXS 0.8537
178 6SY 0.8537
179 2GE 0.8529
180 5ID 0.8524
181 3BH 0.8521
Ligand no: 2; Ligand: GDP ALF; Similar ligands found: 15
No: Ligand Similarity coefficient
1 BEF GDP 0.9660
2 ATP 0.9646
3 ADP 0.9644
4 ANP 0.9557
5 ADP ALF 0.9550
6 ACP 0.9543
7 AGS 0.9520
8 DTP 0.9469
9 ADP AF3 0.9225
10 GDP MG 0.9217
11 ATF 0.8998
12 UTP 0.8949
13 CTP 0.8876
14 DSZ 0.8744
15 AMO 0.8739
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1RJ9; Ligand: GCP; Similar sites found with APoc: 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 Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1RJ9; Ligand: GCP; 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: 1rj9.bio1) has 69 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback