Receptor
PDB id Resolution Class Description Source Keywords
3GJ0 1.48 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF HUMAN RANGDP HOMO SAPIENS G PROTEIN GDP ACETYLATION CYTOPLASM GTP-BINDING HOST- VIRUS INTERACTION NUCLEOTIDE-BINDING NUCLEUS PHOSPHOPROTEIN POLYMORPHISM PROTEIN TRANSPORT TRANSPORTTRANSPORT 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;
B:217;
Valid;
Valid;
none;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
MG A:301;
B:301;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3GJ0 1.48 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF HUMAN RANGDP HOMO SAPIENS G PROTEIN GDP ACETYLATION CYTOPLASM GTP-BINDING HOST- VIRUS INTERACTION NUCLEOTIDE-BINDING NUCLEUS PHOSPHOPROTEIN POLYMORPHISM PROTEIN TRANSPORT TRANSPORTTRANSPORT PROTEIN
Ref.: CRYSTALLOGRAPHIC AND BIOCHEMICAL ANALYSIS OF THE RAN-BINDING ZINC FINGER DOMAIN. J.MOL.BIOL. V. 391 375 2009
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 253 families.
1 5CIT - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 3GJ0 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 5CIW - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 1QG2 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 5CJ2 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
6 5CIQ - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
7 3RAN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
8 1QG4 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 1BYU - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 209 families.
1 5CIT - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 3GJ0 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 5CIW - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 1QG2 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 5CJ2 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
6 5CIQ - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
7 3RAN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
8 1QG4 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 1BYU - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 173 families.
1 5CIT - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 3GJ0 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 5CIW - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 1QG2 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 5CJ2 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
6 5CIQ - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
7 3RAN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
8 1QG4 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 1BYU - 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 : 3GJ0; Ligand: GDP; Similar sites found with APoc: 114
This union binding pocket(no: 1) in the query (biounit: 3gj0.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 3TK1 GDP 2.71493
2 4J0Q GDP 3.16742
3 3WXM GTP 3.16742
4 2C78 GNP 3.16742
5 5W7Q GDP 3.16742
6 1SKQ GDP 3.16742
7 5W75 GDP 3.16742
8 3VMF GTP 3.61991
9 2RCN GDP 4.0724
10 2AWN ADP 4.97738
11 1KK1 GNP 6.33484
12 1YRB GDP 6.78733
13 3WY9 GDP 6.78733
14 3WYA GDP 6.78733
15 3CNL GNP 6.78733
16 1Y3A GDP 7.23982
17 3CX8 GSP 7.69231
18 6AU6 GDP 8.1448
19 1PUJ GNP 8.59729
20 2WJH GDP 9.03614
21 2QN6 GDP 9.50226
22 2WJG GDP 10.1064
23 3U6B GDP 10.4072
24 4P3Y GDP 10.4072
25 2HCJ GDP 10.4072
26 1D8T GDP 10.4072
27 5JBQ GDP 10.4072
28 4G5G GDP 10.4072
29 3U6K GDP 10.4072
30 6CRK GDP 11.3122
31 5GOE GDP 11.7647
32 5CK5 GDP 12.2172
33 5HCN GCP 12.6697
34 1G7S GDP 12.6697
35 5FG3 GDP 13.1222
36 1TQ4 GDP 13.5747
37 4B47 GDP 14.0271
38 5M04 GDP 14.4796
39 2X77 GDP 19.5767
40 1CS4 GSP 20.7547
41 3DOE GTP 20.8333
42 3AQ4 GDP 21.1957
43 1D2E GDP 21.267
44 1KSH GDP 21.5054
45 1F6B GDP 21.7172
46 1MKY GDP 21.7195
47 1MR3 G3D 22.0994
48 1O3Y GTP 22.2892
49 1J2J GTP 22.2892
50 4YLG GDP 22.5434
51 5W76 GDP 22.6244
52 1RE0 GDP 23.1707
53 1S9D GDP 23.1707
54 4DCT GDP 24.4344
55 3N5C GDP 24.6914
56 2W83 GTP 24.8485
57 2WKQ GTP 28.5068
58 2QTV GNP 28.7425
59 1FZQ GDP 29.2818
60 1YZG GDP 29.6089
61 2J0V GDP 29.717
62 1ZJ6 G3D 30.4813
63 3T12 GDP ALF 30.8081
64 3T5G GDP 32.0442
65 1RYH GNP 32.5123
66 1DS6 GDP 33.3333
67 1E96 GTP 33.3333
68 1I4D GDP 33.8542
69 2W2X GSP 34.0541
70 4D0N GDP 35.1351
71 6BC0 GSP 35.1351
72 2WMO GTP 35.7895
73 1G4U GDP 35.8696
74 2FJU GSP 36.5169
75 4YC7 GNP 37.0166
76 1MH1 GNP 37.0968
77 4DID GDP 37.8238
78 5YT0 GDP 38.0952
79 1R4A GNP 38.7879
80 5EE5 GTP 39.1813
81 1ZD9 GDP 39.3617
82 4DKX GDP 41.6667
83 2ZEJ GDP 42.3913
84 1OIX GDP 42.4084
85 4U5X GNP 42.6966
86 1OIV GDP 42.9319
87 3CPJ GDP 42.9864
88 2CJW GDP 43.75
89 5TB5 GDP 43.7838
90 5TAR GDP 43.7838
91 2A9K GDP 44.9198
92 3Q85 GNP 45.5621
93 5JCZ GDP 45.8101
94 5UPK GNP 45.9459
95 3BC1 GNP 46.1538
96 1VG0 GDP 46.3768
97 3Q72 GNP 46.988
98 3RWO GDP 47.027
99 2A5J GDP 47.1204
100 2C5L GTP 47.3988
101 1ZC3 GNP 47.4286
102 5SZH GNP 47.7833
103 1UAD GNP 48
104 1CLU DBG 48.7952
105 5E95 GDP 48.8095
106 1G16 GDP 48.8235
107 2HT6 GDP 48.8506
108 5OEC GDP 49.1803
109 1U8Z GDP 49.4048
110 1Z0J GTP 49.4118
111 5O74 GDP 49.4444
112 1KY3 GDP 49.4506
113 1YVD GNP 49.7041
114 5WDR GNP 49.7076
Pocket No.: 2; Query (leader) PDB : 3GJ0; 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: 3gj0.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
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