Receptor
PDB id Resolution Class Description Source Keywords
3GJ7 1.93 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF HUMAN RANGDP-NUP153ZNF12 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;
A:304;
A:306;
C:301;
C:303;
C:305;
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...
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
3GJ7 1.93 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF HUMAN RANGDP-NUP153ZNF12 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 3GJ7 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 247 families.
1 3GJ7 - 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 209 families.
1 3GJ7 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 3GJ8 - 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 : 3GJ7; Ligand: GDP; Similar sites found with APoc: 187
This union binding pocket(no: 1) in the query (biounit: 3gj7.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 1SVI GDP 3.58974
2 3TK1 GDP 4.0724
3 4ZKD GDP 4.52489
4 2RCN GDP 5.10204
5 4J0Q GDP 5.10204
6 5W75 GDP 5.10204
7 1WF3 GNP 5.88235
8 3VMF GTP 6.12245
9 3WXM GTP 6.12245
10 2XTZ GSP 6.33484
11 6G14 G4P 6.33484
12 1PUJ GNP 6.33484
13 3EC1 GDP 6.78733
14 1TAD ALF 6.78733
15 1TAD GDP 6.78733
16 3CNL GNP 6.78733
17 3CX8 GSP 7.69231
18 1ZCB GDP 7.69231
19 1CS4 GSP 8.1448
20 4NON GDP 9.04977
21 2ODE ALF GDP 9.04977
22 6AU6 GDP 9.04977
23 2WJH GDP 9.63855
24 1SVK ALF GDP 9.95475
25 1BH2 GSP 9.95475
26 3WY9 GDP 10.2041
27 3WYA GDP 10.2041
28 2WJG GDP 10.6383
29 3U6B GDP 11.2245
30 1D8T GDP 11.2245
31 2BVN GNP 11.2245
32 4LC1 GDP 11.2245
33 5JBQ GDP 11.2245
34 4P3Y GDP 11.2245
35 4G5G GDP 11.2245
36 3MD0 GDP 11.2245
37 3U6K GDP 11.2245
38 4PC3 GDP 11.2245
39 5GOE GDP 11.7647
40 5CK5 GDP 12.2172
41 1YRB GDP 12.2449
42 2C78 GNP 12.2449
43 2C77 GNP 12.2449
44 3AB3 GDP 12.2449
45 5HCN GCP 12.6697
46 5W7Q GDP 13.2653
47 1TQ4 GDP 13.5747
48 1Y3A GDP 15.3846
49 5M04 GDP 18.3673
50 6CRK GDP 18.3673
51 2X77 GDP 19.5767
52 4M9Q GNP 20.8145
53 3DOE GTP 20.8333
54 1UPT GTP 21.0526
55 3AQ4 GDP 21.1957
56 1KSH GDP 21.5054
57 1F6B GDP 21.7172
58 1MKY GDP 21.7195
59 1MR3 G3D 22.0994
60 2J59 GTP 22.2892
61 1O3Y GTP 22.2892
62 1J2J GTP 22.2892
63 4YLG GDP 22.5434
64 5W76 GDP 22.6244
65 2WIC GNP 23.0769
66 1RE0 GDP 23.1707
67 1S9D GDP 23.1707
68 2A5F GTP 24
69 4DCT GDP 24.4344
70 3PCR GTP 24.6914
71 1M2O GNP 25.2632
72 3N5C GDP 25.3086
73 2W83 GTP 25.4545
74 2WKQ GTP 28.0543
75 4ZI2 GNP 28.4211
76 2QTV GNP 28.7425
77 2GJ8 ALF GDP 29.0698
78 2J0V GDP 29.2453
79 1FZQ GDP 29.2818
80 1YZG GDP 29.6089
81 1ZJ6 G3D 30.4813
82 3T12 GDP ALF 30.8081
83 3REF GDP 30.9278
84 3T5G GDP 31.4917
85 1RYH GNP 32.0197
86 6BSX E7S 32.0225
87 6BSX GDP 32.0225
88 1DS6 GDP 32.8125
89 1E96 GTP 32.8125
90 1I4D GDP 33.3333
91 2W2X GSP 33.5135
92 4V0K GDP 33.7278
93 2GCN GDP 33.8308
94 1NF3 GNP 33.8462
95 5XC5 GTP 34.0909
96 1A4R GNH 34.555
97 1A4R GDP 34.555
98 4D0N GDP 34.5946
99 6BCB GSP 34.5946
100 6BCA GSP 34.5946
101 6BC0 GSP 34.5946
102 2NGR GDP 35.0785
103 3LXR GDP 35.1351
104 5HPY GDP 35.1351
105 2WMO GTP 35.2632
106 1G4U GDP 35.3261
107 4XOI GTP 35.5556
108 2FJU GSP 35.9551
109 4XSH GSP 36.3129
110 1KMQ GNP 36.413
111 4YC7 GNP 36.4641
112 1MH1 GNP 36.5591
113 4DID GDP 37.3057
114 3SBD GNP 37.9679
115 1R4A GNP 38.7879
116 1ZD9 GDP 38.8298
117 5EE5 GTP 39.1813
118 2G77 GDP 39.899
119 4DKX GDP 41.2037
120 2BCG GDP 41.7476
121 5OCG GNP 41.7989
122 4U5X GNP 42.1348
123 2F9L GDP 42.2111
124 1OIX GDP 42.4084
125 3CPJ GDP 42.5339
126 5UQW GDP 42.8571
127 1OIV GDP 42.9319
128 5TAR GDP 43.2432
129 5TB5 GDP 43.2432
130 5SZH GNP 43.3498
131 2ZEJ GDP 44.0217
132 2CJW GDP 44.2708
133 2A9K GDP 44.385
134 5JCZ GDP 45.2514
135 5UPK GNP 45.4054
136 1Z06 GNP 45.5026
137 3BC1 GNP 45.641
138 2EW1 GNP 45.7711
139 1VG0 GDP 45.8937
140 1VG8 GNP 45.8937
141 3Q85 GNP 46.1538
142 4LX0 BEF GDP 46.3277
143 1YZN GNP 46.4865
144 3RWO GDP 46.4865
145 2HV8 GTP 46.5116
146 2A5J GDP 46.5969
147 2C5L GTP 46.8208
148 1ZC3 GNP 46.8571
149 5LEF GTP 47.1204
150 2D7C GTP 47.3054
151 5O2T GSP 47.3373
152 1UAD GNP 47.4286
153 5WLB GNP 47.5904
154 3Q72 GNP 47.5904
155 2UZI GTP 48.1928
156 1CLU DBG 48.1928
157 5E95 GDP 48.2143
158 1G16 GDP 48.2353
159 1X1R GDP 48.3146
160 3TKL GTP 48.4694
161 6D5L GNP 48.503
162 1LFD GNP 48.503
163 6D5J GNP 48.503
164 6D59 GNP 48.503
165 6BVJ GNP 48.503
166 6D55 GNP 48.503
167 6BVL GNP 48.503
168 6D5H GNP 48.503
169 6BVM GNP 48.503
170 6D5E GNP 48.503
171 6D56 GNP 48.503
172 6BVI GNP 48.503
173 6BVK GNP 48.503
174 6D5V GNP 48.503
175 6D5G GNP 48.503
176 4C4P GNP 48.5549
177 5OEC GDP 48.6339
178 3KUD GDP 48.7952
179 1WQ1 GDP 48.7952
180 1U8Z GDP 48.8095
181 1Z0J GTP 48.8235
182 5O74 GDP 48.8889
183 1KY3 GDP 48.9011
184 1YVD GNP 49.1124
185 3DDC GNP 49.3976
186 2HT6 GDP 49.4253
187 2FFQ GSP 49.7076
188 3QBT GNP 50
189 4LHW GNP 50
190 4KVG GTP 50
191 1Z0A GDP 50
Pocket No.: 2; Query (leader) PDB : 3GJ7; 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: 3gj7.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
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