Receptor
PDB id Resolution Class Description Source Keywords
4ZKD 2.18 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE S. CEREVISIAE SKI7 GTPASE-LIKE DOMA TO GDP AND INORGANIC PHOSPHATE. SACCHAROMYCES CEREVISIAE GTPASE TRANSLATION NGD SKI HYDROLASE GTP-BINDING PROTEI
Ref.: SACCHAROMYCES CEREVISIAE SKI7 IS A GTP-BINDING PROT ADOPTING THE CHARACTERISTIC CONFORMATION OF ACTIVE TRANSLATIONAL GTPASES. STRUCTURE V. 23 1336 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PO4 A:801;
Invalid;
none;
submit data
94.971 O4 P [O-]P...
MG A:803;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
GDP A:802;
Valid;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4ZKD 2.18 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE S. CEREVISIAE SKI7 GTPASE-LIKE DOMA TO GDP AND INORGANIC PHOSPHATE. SACCHAROMYCES CEREVISIAE GTPASE TRANSLATION NGD SKI HYDROLASE GTP-BINDING PROTEI
Ref.: SACCHAROMYCES CEREVISIAE SKI7 IS A GTP-BINDING PROT ADOPTING THE CHARACTERISTIC CONFORMATION OF ACTIVE TRANSLATIONAL GTPASES. STRUCTURE V. 23 1336 2015
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 4ZKE - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
2 4ZKD - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 4ZKE - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
2 4ZKD - 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 1039 families.
1 4ZKE - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
2 4ZKD - 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 : 4ZKD; Ligand: GDP; Similar sites found with APoc: 75
This union binding pocket(no: 1) in the query (biounit: 4zkd.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 4RD0 GDP 2.89157
2 3EC1 GDP 2.98103
3 3RAB GNP 3.5503
4 5UWP GNP 4.21941
5 5DIF GNP 4.21941
6 5UWW GNP 4.21941
7 5UWQ GNP 4.21941
8 5UWU GNP 4.21941
9 6CIT GNP 4.21941
10 5UWO GNP 4.21941
11 5UWI GNP 4.21941
12 5UWR GNP 4.21941
13 5DHF GNP 4.21941
14 5UWT GNP 4.21941
15 5UWJ GNP 4.21941
16 5UWH GNP 4.21941
17 1YZN GNP 4.32432
18 6G14 G4P 4.42177
19 4LC1 GDP 4.45104
20 2GCO GNP 4.47761
21 3GJ7 GDP 4.52489
22 1IBR GNP 4.62963
23 4HAT GNP 4.62963
24 2WIC GNP 4.86891
25 1YRB GDP 4.96183
26 1WA5 GTP 5.11364
27 2HT6 GDP 5.17241
28 1Z06 GNP 5.29101
29 5BXQ GDP 5.51181
30 5O74 GDP 5.55556
31 1S8F GDP 5.64972
32 4M9Q GNP 5.72687
33 3QBT GNP 5.74713
34 1Z0A GDP 5.74713
35 1A4R GNH 5.75916
36 3CH5 GDP 5.76923
37 3Q72 GNP 6.0241
38 3GJ3 GDP 6.06061
39 2A5F GTP 6.28571
40 2QN6 GDP 6.45161
41 1FZQ GDP 6.62983
42 1RE0 GDP 6.70732
43 1EK0 GNP 7.05882
44 1I4D GDP 7.14286
45 2BME GNP 7.52688
46 1TU3 GNP 7.60234
47 4DCT GDP 7.67544
48 4NCN GTP 7.87746
49 1Z0J GTP 8.23529
50 2FFQ GSP 8.77193
51 2G77 GDP 8.78049
52 2G77 AF3 8.78049
53 5FG3 GDP 8.81764
54 3GJ4 GDP 9.09091
55 1F6B GDP 9.59596
56 1YZQ GNP 10
57 1KSH GDP 11.1842
58 5YT0 GDP 12.0879
59 2WJG GDP 13.8298
60 3GJ5 GDP 14.7059
61 2BVN GNP 15.5216
62 1ZJ6 G3D 16.0428
63 1KK1 GNP 19.0244
64 1G7C 5GP 20.9607
65 5CK5 GDP 21.8354
66 1VG8 GNP 23.1884
67 1VG1 GDP 25.9459
68 3MJH GTP 26.4706
69 1LFD GNP 29.3413
70 3WXM GTP 30.4251
71 1SKQ GDP 31.2644
72 2FH5 GTP 31.3084
73 5UWS GNP 31.8182
74 2C78 GNP 36.5432
75 2C77 GNP 36.5432
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