Receptor
PDB id Resolution Class Description Source Keywords
5H7K 1.6 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF ELONGATION FACTOR 2 GDP-FORM PYROCOCCUS HORIKOSHII OT3 ELONGATION FACTOR PROTEIN BIOSYNTHESIS GTP-BINDING TRANSL
Ref.: THE C-TERMINAL HELIX OF RIBOSOMAL P STALK RECOGNIZE HYDROPHOBIC GROOVE OF ELONGATION FACTOR 2 IN A NOVE NUCLEIC ACIDS RES. V. 46 3232 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:501;
Valid;
none;
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443.201 C10 H15 N5 O11 P2 c1nc2...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5H7K 1.6 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF ELONGATION FACTOR 2 GDP-FORM PYROCOCCUS HORIKOSHII OT3 ELONGATION FACTOR PROTEIN BIOSYNTHESIS GTP-BINDING TRANSL
Ref.: THE C-TERMINAL HELIX OF RIBOSOMAL P STALK RECOGNIZE HYDROPHOBIC GROOVE OF ELONGATION FACTOR 2 IN A NOVE NUCLEIC ACIDS RES. V. 46 3232 2018
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 5H7K - 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 1331 families.
1 5H7K - 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 1144 families.
1 5H7K - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GDP; Similar ligands found: 160
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 GNP 0.839506 0.973684
6 9GM 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 GDD 0.747253 0.961039
19 GKE 0.747253 0.961039
20 GPG 0.741573 0.961039
21 GDP BEF 0.741176 0.935065
22 GTP MG 0.732558 0.96
23 G3D 0.732558 0.986486
24 ALF 5GP 0.729412 0.888889
25 Y9Z 0.728261 0.902439
26 G5P 0.723404 0.973684
27 GFB 0.72043 0.961039
28 GTG 0.72043 0.936709
29 GDR 0.72043 0.961039
30 G4P 0.715909 0.986486
31 6CK 0.712766 0.936709
32 G3A 0.712766 0.973684
33 GDP ALF 0.7 0.888889
34 GDP AF3 0.7 0.888889
35 YGP 0.698925 0.901235
36 GKD 0.697917 0.961039
37 JB2 0.697917 0.961039
38 GDX 0.690722 0.973684
39 GPD 0.690722 0.925
40 GMP 0.684211 0.88
41 0O2 0.666667 0.986486
42 JB3 0.656863 0.948718
43 NGD 0.650485 0.961039
44 GDP 7MG 0.636364 0.911392
45 DGI 0.636364 0.923077
46 U2G 0.634615 0.936709
47 GPX 0.634409 0.946667
48 IDP 0.632184 0.972973
49 2MD 0.632075 0.891566
50 CAG 0.62963 0.880952
51 KB7 0.629214 0.82716
52 CG2 0.622642 0.936709
53 FEG 0.619048 0.879518
54 MGD 0.614679 0.891566
55 ZGP 0.613208 0.869048
56 GH3 0.612903 0.973333
57 3GP 0.611765 0.946667
58 MD1 0.607143 0.891566
59 PGD 0.59292 0.925
60 DGT 0.591398 0.923077
61 BGO 0.588785 0.924051
62 TPG 0.582609 0.840909
63 DBG 0.582609 0.948718
64 KBD 0.581633 0.82716
65 QBQ 0.576087 0.986486
66 2GP 0.574713 0.96
67 FE9 0.570175 0.776596
68 KBJ 0.558824 0.797619
69 MGP 0.553191 0.961039
70 G4M 0.548387 0.880952
71 6G0 0.547368 0.961039
72 I2C FE2 CMO CMO 0.543103 0.808989
73 G1R G1R 0.542373 0.924051
74 P2G 0.527473 0.883117
75 PGD O 0.525 0.850575
76 ADP 0.522222 0.92
77 R5I 0.520833 0.946667
78 R7I 0.520833 0.946667
79 GGM 0.517544 0.901235
80 DG 0.516484 0.910256
81 DGP 0.516484 0.910256
82 P1G 0.516129 0.871795
83 CZF 0.515789 0.933333
84 G1G 0.508475 0.925
85 IMP 0.505495 0.959459
86 AKW 0.504425 0.890244
87 G C 0.504348 0.9
88 GPC 0.491525 0.879518
89 G7M 0.483871 0.948052
90 6AD 0.479592 0.841463
91 ATP 0.473684 0.92
92 HEJ 0.473684 0.92
93 G2Q 0.471154 0.961039
94 AQP 0.46875 0.92
95 5FA 0.46875 0.92
96 GTA 0.468468 0.936709
97 7DD 0.468085 0.906667
98 SGP 0.463158 0.82716
99 01G 0.462963 0.902439
100 HFD 0.459184 0.873418
101 JSQ 0.459184 0.873418
102 B4P 0.457447 0.894737
103 AP5 0.457447 0.894737
104 A2D 0.456522 0.894737
105 6YZ 0.455446 0.896104
106 ACQ 0.454545 0.896104
107 ANP 0.454545 0.896104
108 5GP 5GP 0.454545 0.883117
109 AT4 0.452632 0.884615
110 APC G U 0.451613 0.886076
111 PRT 0.449541 0.959459
112 ITT 0.447917 0.868421
113 BA3 0.446809 0.894737
114 C2E 0.444444 0.921053
115 35G 0.444444 0.933333
116 PCG 0.444444 0.933333
117 MGO 0.441176 0.864198
118 AN2 0.4375 0.907895
119 NO7 0.436893 0.860759
120 M33 0.43299 0.883117
121 UCG 0.429688 0.911392
122 ACP 0.428571 0.896104
123 MGQ 0.424528 0.935897
124 APR 0.424242 0.894737
125 7DT 0.424242 0.906667
126 AR6 0.424242 0.894737
127 M7G A2M G 0.422819 0.808989
128 93A 0.42268 0.833333
129 A4P 0.420168 0.869048
130 G8D 0.42 0.875
131 AD9 0.42 0.896104
132 AGS 0.42 0.873418
133 CA0 0.418367 0.896104
134 ATF 0.417476 0.884615
135 NYZ 0.415842 0.935897
136 GZ0 0.415254 0.948718
137 AGO 0.414634 0.888889
138 KG4 0.414141 0.896104
139 NIA 0.413043 0.82716
140 MGV 0.412844 0.890244
141 TAT 0.411765 0.884615
142 T99 0.411765 0.884615
143 ADQ 0.411215 0.871795
144 A1R 0.411215 0.839506
145 RGT 0.410714 0.909091
146 CGP 0.409836 0.86747
147 HQG 0.409524 0.907895
148 C1Z 0.409091 0.986486
149 AMP 0.408602 0.893333
150 A 0.408602 0.893333
151 UP5 0.40678 0.873418
152 C2R 0.406593 0.906667
153 AMZ 0.406593 0.918919
154 JBT 0.405882 0.778947
155 A22 0.40566 0.907895
156 25L 0.405405 0.907895
157 ADX 0.40404 0.809524
158 8OD 0.401961 0.946667
159 50T 0.4 0.883117
160 4TC 0.4 0.851852
Similar Ligands (3D)
Ligand no: 1; Ligand: GDP; Similar ligands found: 93
No: Ligand Similarity coefficient
1 ADP MG 0.9864
2 GDP MG 0.9797
3 DAT 0.9680
4 ALF GDP 0.9549
5 A12 0.9524
6 BEF GDP 0.9486
7 AU1 0.9476
8 CUU 0.9442
9 SON 0.9417
10 TYD 0.9414
11 M7G 0.9411
12 ADP ALF 0.9391
13 ADP BEF 0.9391
14 ADP AF3 0.9391
15 BEF ADP 0.9383
16 GAP 0.9328
17 O02 0.9303
18 G5A 0.9285
19 AP2 0.9265
20 5AL 0.9252
21 8GD 0.9250
22 M7M 0.9212
23 AV2 0.9211
24 DAL AMP 0.9209
25 PRX 0.9194
26 UDP 0.9193
27 8LE 0.9188
28 SRP 0.9155
29 SAM 0.9145
30 A5A 0.9126
31 GJV 0.9116
32 NWZ 0.9106
33 CDP 0.9093
34 MGT 0.9090
35 YYY 0.9086
36 5CA 0.9069
37 XMP 0.9066
38 EO7 0.9060
39 SSA 0.9052
40 DSH 0.9051
41 71V 0.9041
42 2A5 0.8973
43 TBD 0.8937
44 CDP MG 0.8931
45 SAH 0.8927
46 IMU 0.8919
47 6RE 0.8917
48 J7C 0.8916
49 7D3 0.8915
50 8LH 0.8914
51 DUD 0.8888
52 NX8 0.8885
53 6CG 0.8882
54 ABM 0.8881
55 8X1 0.8861
56 FMP 0.8855
57 LMS 0.8847
58 8GM 0.8842
59 DTP 0.8842
60 D4D 0.8817
61 C8M 0.8813
62 EEM 0.8812
63 SFG 0.8795
64 8OP 0.8780
65 ADP PO3 0.8775
66 D5M 0.8773
67 IRP 0.8767
68 PAP 0.8765
69 HDV 0.8759
70 ATR 0.8755
71 APC 0.8746
72 N5O 0.8734
73 A3N 0.8728
74 AS 0.8705
75 ATY 0.8684
76 54H 0.8676
77 TSB 0.8674
78 ME8 0.8672
79 HF7 0.8667
80 6MA 0.8654
81 SAI 0.8651
82 DUN 0.8649
83 LSS 0.8640
84 5FU 0.8638
85 P5A 0.8634
86 8QN 0.8633
87 DZ4 0.8609
88 CNU 0.8603
89 NVA LMS 0.8600
90 FNU 0.8593
91 TKW 0.8580
92 MOD 0.8567
93 MSP 0.8549
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5H7K; Ligand: GDP; Similar sites found with APoc: 131
This union binding pocket(no: 1) in the query (biounit: 5h7k.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 1YZQ GNP 2.35294
2 2FFQ GSP 2.92398
3 1VG8 GNP 3.38164
4 1VG8 GNP 3.38164
5 1VG8 GNP 3.38164
6 1VG8 GNP 3.38164
7 1SVK ALF GDP 3.39943
8 6MHE GDP 3.42857
9 1Y3A GDP 3.64742
10 1Y3A GDP 3.64742
11 1Y3A GDP 3.64742
12 1Y3A GDP 3.64742
13 1TAD GDP 3.7037
14 1TAD ALF 3.7037
15 1VG1 GDP 3.78378
16 1BH2 GSP 3.80952
17 1O3Y GTP 4.21687
18 1O3Y GTP 4.21687
19 1CS4 GSP 4.24528
20 1ZD9 GDP 4.25532
21 1RE0 GDP 4.26829
22 1ZJ6 G3D 4.27807
23 1ZJ6 G3D 4.27807
24 1ZJ6 G3D 4.27807
25 2A5F GTP 4.66321
26 3AB3 GDP 4.87805
27 3AB3 GDP 4.87805
28 6AU6 GDP 5.03979
29 5Z2M GTP 5.07246
30 1M2O GNP 5.28967
31 1M2O GNP 5.28967
32 1M2O GNP 5.28967
33 1M2O GNP 5.28967
34 2XTZ GSP 5.36723
35 2XTZ GSP 5.36723
36 2XTZ GSP 5.36723
37 1GOT GDP 5.47945
38 3CX8 GSP 6.40394
39 5KDO GDP 6.75676
40 1S9D GDP 7.38916
41 3Q85 GNP 7.69231
42 3Q85 GNP 7.69231
43 6IZW GSP 7.88177
44 3MD0 GDP 7.88732
45 1Z06 GNP 7.93651
46 5M04 GDP 8.06045
47 3T1O GDP 8.08081
48 3T1O GDP 8.08081
49 5GOE GDP 8.31234
50 4DCT GDP 8.56423
51 1Z0A GDP 8.62069
52 1Z0A GDP 8.62069
53 1Z0A GDP 8.62069
54 1Z0A GDP 8.62069
55 1Z0A GDP 8.62069
56 1Z0A GDP 8.62069
57 2GJ8 ALF GDP 8.72093
58 2GJ8 ALF GDP 8.72093
59 1FZQ GDP 8.83978
60 6KX2 GDP 9.39227
61 5BXQ GDP 10.1852
62 5BXQ GDP 10.1852
63 5BXQ GDP 10.1852
64 6G14 G4P 10.2041
65 6G14 G4P 10.2041
66 1KSH GDP 10.2151
67 2ODE ALF GDP 10.2857
68 1PUJ GNP 10.6383
69 3RWO GDP 10.8108
70 3RWO GDP 10.8108
71 2FH5 GTP 11.3514
72 2FH5 GTP 11.3514
73 6A8D GDP 11.4583
74 3T12 GDP ALF 12.5
75 2G77 GDP 12.6263
76 6CRK GDP 12.6761
77 1GP2 GDP 12.6761
78 1YZG GDP 13.4078
79 4V0K GDP 13.6095
80 1R4A GNP 13.7255
81 1R4A GNP 13.7255
82 1R4A GNP 13.7255
83 1MKY GDP 13.8539
84 2OM2 GDP 13.8889
85 5O74 GDP 13.8889
86 2OM2 GDP 13.8889
87 5O74 GDP 13.8889
88 5FG3 GDP 15.1133
89 1F6B GDP 15.1515
90 1F6B GDP 15.1515
91 1FQK GDP 15.6463
92 1FQK GDP 15.6463
93 1YRB GDP 16.4122
94 1FQJ GDP 16.6667
95 4M9Q GNP 16.7401
96 4M9Q GNP 16.7401
97 4M9Q GNP 16.7401
98 1D2E GDP 18.3879
99 1D2E GDP 18.3879
100 1D2E GDP 18.3879
101 1D2E GDP 18.3879
102 4NCN GTP 18.3879
103 4NCN GTP 18.3879
104 2WJG GDP 18.617
105 2WJG GDP 18.617
106 1G7S GDP 18.6398
107 4RD0 GDP 18.6398
108 1KK1 GNP 18.6398
109 2QN6 GDP 18.8917
110 3WXM GTP 19.6809
111 3WXM GTP 19.6809
112 3WXM GTP 19.6809
113 3WXM GTP 19.6809
114 1D8T GDP 20.8651
115 2BVN GNP 20.8651
116 2BVN GNP 20.8651
117 1D8T GDP 20.8651
118 1WF3 GNP 21.2625
119 1SKQ GDP 22.1662
120 1SKQ GDP 22.1662
121 2WJH GDP 22.8916
122 6MHF GDP 25.8065
123 5O2T GSP 26.6272
124 1CLU DBG 27.7108
125 2HT6 GDP 31.6092
126 2HT6 GDP 31.6092
127 2C77 GNP 34.7607
128 2C78 GNP 35.0126
129 2HCJ GDP 35.1351
130 4B47 GDP 37.4656
131 5YT0 GDP 38.0952
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