Receptor
PDB id Resolution Class Description Source Keywords
3GJ5 1.79 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF HUMAN RANGDP-NUP153ZNF4 COMPLEX HOMO SAPIENS G PROTEIN GDP RAN NUP153 NUCLEAR PORE ZINC FINGER ACETYLATION CYTOPLASM GTP-BINDING HOST-VIRUS INTERACTION ISOPEPTIDE BOND NUCLEOTIDE-BINDING NUCLEUS PHOSPHOPROTEIN POLYMORPHISM PROTEIN TRANSPORT TRANSPORTUBL CONJUGATION DNA-BINDING METAL-BINDING MRNA TRANSPORT NUCLEAR PORE COMPLEX TRANSLOCATION ZINC ZINC-FINGER TRANSPORT PROTEIN
Ref.: CRYSTALLOGRAPHIC AND BIOCHEMICAL ANALYSIS OF THE RAN-BINDING ZINC FINGER DOMAIN. J.MOL.BIOL. V. 391 375 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:302;
C:302;
Valid;
Valid;
none;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
MG A:301;
C:301;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
ZN B:300;
D:300;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3GJ5 1.79 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF HUMAN RANGDP-NUP153ZNF4 COMPLEX HOMO SAPIENS G PROTEIN GDP RAN NUP153 NUCLEAR PORE ZINC FINGER ACETYLATION CYTOPLASM GTP-BINDING HOST-VIRUS INTERACTION ISOPEPTIDE BOND NUCLEOTIDE-BINDING NUCLEUS PHOSPHOPROTEIN POLYMORPHISM PROTEIN TRANSPORT TRANSPORTUBL CONJUGATION DNA-BINDING METAL-BINDING MRNA TRANSPORT NUCLEAR PORE COMPLEX TRANSLOCATION ZINC ZINC-FINGER TRANSPORT PROTEIN
Ref.: CRYSTALLOGRAPHIC AND BIOCHEMICAL ANALYSIS OF THE RAN-BINDING ZINC FINGER DOMAIN. J.MOL.BIOL. V. 391 375 2009
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 291 families.
1 3GJ5 - GDP C10 H15 N5 O11 P2 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 247 families.
1 3GJ5 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 3GJ3 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 3GJ4 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 209 families.
1 3GJ5 - 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 : 3GJ5; Ligand: GDP; Similar sites found with APoc: 172
This union binding pocket(no: 1) in the query (biounit: 3gj5.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 4J0Q GDP 3.16742
2 2RCN GDP 4.0724
3 3WXM GTP 4.0724
4 2C78 GNP 4.0724
5 3VMF GTP 4.0724
6 3WY9 GDP 4.0724
7 3TK1 GDP 4.0724
8 3WYA GDP 4.0724
9 2C77 GNP 4.0724
10 5W7Q GDP 4.0724
11 4LC1 GDP 4.52489
12 3MD0 GDP 5.42986
13 1WF3 GNP 5.88235
14 2XTZ GSP 6.33484
15 6G14 G4P 6.33484
16 3EC1 GDP 6.78733
17 1TAD GDP 6.78733
18 1TAD ALF 6.78733
19 3CX8 GSP 7.69231
20 3AB3 GDP 7.69231
21 1CS4 GSP 8.1448
22 1YRB GDP 8.82353
23 6AU6 GDP 9.04977
24 2ODE ALF GDP 9.04977
25 4NON GDP 9.04977
26 1SVK ALF GDP 9.95475
27 1BH2 GSP 9.95475
28 3U6B GDP 10.4072
29 2BVN GNP 10.4072
30 1D8T GDP 10.4072
31 5JBQ GDP 10.4072
32 4P3Y GDP 10.4072
33 4G5G GDP 10.4072
34 3U6K GDP 10.4072
35 5W75 GDP 11.7647
36 5HCN GCP 12.6697
37 1TQ4 GDP 13.5747
38 4ZKD GDP 14.7059
39 5CK5 GDP 14.7059
40 5GOE GDP 14.7059
41 5M04 GDP 17.6471
42 2X77 GDP 19.5767
43 4M9Q GNP 20.8145
44 3DOE GTP 20.8333
45 1UPT GTP 21.0526
46 3AQ4 GDP 21.1957
47 1KSH GDP 21.5054
48 1F6B GDP 21.7172
49 1MKY GDP 21.7195
50 1MR3 G3D 22.0994
51 2J59 GTP 22.2892
52 1O3Y GTP 22.2892
53 1J2J GTP 22.2892
54 4YLG GDP 22.5434
55 5W76 GDP 22.6244
56 1RE0 GDP 23.1707
57 1S9D GDP 23.1707
58 2A5F GTP 24
59 4DCT GDP 24.4344
60 3PCR GTP 24.6914
61 1M2O GNP 25.2632
62 3N5C GDP 25.3086
63 2W83 GTP 25.4545
64 1PUJ GNP 26.4706
65 4PC3 GDP 26.4706
66 2WKQ GTP 28.0543
67 4ZI2 GNP 28.4211
68 2QTV GNP 28.7425
69 2GJ8 ALF GDP 29.0698
70 2J0V GDP 29.2453
71 1FZQ GDP 29.2818
72 1YZG GDP 29.6089
73 1ZJ6 G3D 30.4813
74 3T12 GDP ALF 30.8081
75 3T5G GDP 31.4917
76 1RYH GNP 32.0197
77 6BSX E7S 32.0225
78 6BSX GDP 32.0225
79 4BAS GNP 32.1608
80 1E96 GTP 32.8125
81 1DS6 GDP 32.8125
82 1I4D GDP 33.3333
83 4V0K GDP 33.7278
84 2GCN GDP 33.8308
85 1NF3 GNP 33.8462
86 5XC5 GTP 34.0909
87 1A4R GNH 34.555
88 1A4R GDP 34.555
89 4D0N GDP 34.5946
90 6BCA GSP 34.5946
91 6BCB GSP 34.5946
92 6BC0 GSP 34.5946
93 3LXR GDP 35.1351
94 2FJU GSP 35.9551
95 4XSH GSP 36.3129
96 1KMQ GNP 36.413
97 4YC7 GNP 36.4641
98 1MH1 GNP 36.5591
99 3SBD GNP 37.9679
100 1R4A GNP 38.7879
101 1ZD9 GDP 38.8298
102 5EE5 GTP 39.1813
103 2G77 GDP 39.899
104 4DKX GDP 41.2037
105 2BCG GDP 41.7476
106 5OCG GNP 41.7989
107 4U5X GNP 42.1348
108 2F9L GDP 42.2111
109 1OIX GDP 42.4084
110 3CPJ GDP 42.5339
111 5UQW GDP 42.8571
112 1OIV GDP 42.9319
113 5TAR GDP 43.2432
114 5TB5 GDP 43.2432
115 5SZH GNP 43.3498
116 2ZEJ GDP 44.0217
117 2CJW GDP 44.2708
118 2A9K GDP 44.385
119 5JCZ GDP 45.2514
120 5UPK GNP 45.4054
121 1Z06 GNP 45.5026
122 3BC1 GNP 45.641
123 2EW1 GNP 45.7711
124 1VG8 GNP 45.8937
125 1VG0 GDP 45.8937
126 3Q85 GNP 46.1538
127 4LX0 BEF GDP 46.3277
128 1YZN GNP 46.4865
129 3RWO GDP 46.4865
130 2HV8 GTP 46.5116
131 2A5J GDP 46.5969
132 2C5L GTP 46.8208
133 1ZC3 GNP 46.8571
134 5LEF GTP 47.1204
135 2D7C GTP 47.3054
136 5O2T GSP 47.3373
137 1UAD GNP 47.4286
138 5WLB GNP 47.5904
139 3Q72 GNP 47.5904
140 1CLU DBG 48.1928
141 2UZI GTP 48.1928
142 5E95 GDP 48.2143
143 1G16 GDP 48.2353
144 1X1R GDP 48.3146
145 3TKL GTP 48.4694
146 6BVL GNP 48.503
147 6D5L GNP 48.503
148 6BVI GNP 48.503
149 6BVM GNP 48.503
150 6BVJ GNP 48.503
151 6D59 GNP 48.503
152 6BVK GNP 48.503
153 6D56 GNP 48.503
154 6D5J GNP 48.503
155 6D5H GNP 48.503
156 6D5E GNP 48.503
157 6D55 GNP 48.503
158 1LFD GNP 48.503
159 6D5V GNP 48.503
160 6D5G GNP 48.503
161 4C4P GNP 48.5549
162 5OEC GDP 48.6339
163 3KUD GDP 48.7952
164 1WQ1 GDP 48.7952
165 1U8Z GDP 48.8095
166 1Z0J GTP 48.8235
167 5O74 GDP 48.8889
168 1KY3 GDP 48.9011
169 1YVD GNP 49.1124
170 3DDC GNP 49.3976
171 2HT6 GDP 49.4253
172 2FFQ GSP 49.7076
173 3QBT GNP 50
174 1Z0A GDP 50
175 4LHW GNP 50
176 4KVG GTP 50
Pocket No.: 2; Query (leader) PDB : 3GJ5; 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: 3gj5.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
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