Receptor
PDB id Resolution Class Description Source Keywords
1SVI 1.95 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF THE GTP-BINDING PROTEIN YSXC COMPLEXED BACILLUS SUBTILIS YSXC ENGB GTPASE GTP-BINDING PROTEIN GDP HYDROLASE
Ref.: ANALYSIS OF THE OPEN AND CLOSED CONFORMATIONS OF TH GTP-BINDING PROTEIN YSXC FROM BACILLUS SUBTILIS. J.MOL.BIOL. V. 339 265 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:401;
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
1SVI 1.95 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF THE GTP-BINDING PROTEIN YSXC COMPLEXED BACILLUS SUBTILIS YSXC ENGB GTPASE GTP-BINDING PROTEIN GDP HYDROLASE
Ref.: ANALYSIS OF THE OPEN AND CLOSED CONFORMATIONS OF TH GTP-BINDING PROTEIN YSXC FROM BACILLUS SUBTILIS. J.MOL.BIOL. V. 339 265 2004
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 283 families.
1 1SVI - 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 235 families.
1 1SVI - 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 319 families.
1 1SVI - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 3PQC - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GDP; Similar ligands found: 168
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 GKE 0.747253 0.961039
18 GDD 0.747253 0.961039
19 GDC 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 GDR 0.72043 0.961039
26 GFB 0.72043 0.961039
27 GTG 0.72043 0.936709
28 G4P 0.715909 0.986486
29 6CK 0.712766 0.936709
30 G3A 0.712766 0.973684
31 GDP AF3 0.7 0.888889
32 GDP ALF 0.7 0.888889
33 ALF GDP 0.7 0.888889
34 YGP 0.698925 0.901235
35 JB2 0.697917 0.961039
36 GKD 0.697917 0.961039
37 GPD 0.690722 0.925
38 GDX 0.690722 0.973684
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 GDP 7MG 0.636364 0.911392
44 DGI 0.636364 0.923077
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 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 2GP 0.574713 0.96
66 FE9 0.570175 0.776596
67 GCP G 0.56 0.921053
68 KBJ 0.558824 0.797619
69 G A A A 0.553571 0.923077
70 A G 0.553571 0.935065
71 MGP 0.553191 0.961039
72 U A G G 0.548673 0.935065
73 G4M 0.548387 0.880952
74 6G0 0.547368 0.961039
75 G1R G1R 0.542373 0.924051
76 P2G 0.527473 0.883117
77 PGD O 0.525 0.850575
78 ADP 0.522222 0.92
79 R5I 0.520833 0.946667
80 R7I 0.520833 0.946667
81 GGM 0.517544 0.901235
82 DGP 0.516484 0.910256
83 DG 0.516484 0.910256
84 P1G 0.516129 0.871795
85 G U 0.513274 0.9
86 G1G 0.508475 0.925
87 IMP 0.505495 0.959459
88 AKW 0.504425 0.890244
89 G C 0.504348 0.9
90 GPC 0.491525 0.879518
91 G7M 0.483871 0.948052
92 6AD 0.479592 0.841463
93 ATP 0.473684 0.92
94 HEJ 0.473684 0.92
95 G2Q 0.471154 0.961039
96 AQP 0.46875 0.92
97 5FA 0.46875 0.92
98 GTA 0.468468 0.936709
99 7DD 0.468085 0.906667
100 G G G RPC 0.466102 0.875
101 SGP 0.463158 0.82716
102 01G 0.462963 0.902439
103 JSQ 0.459184 0.873418
104 HFD 0.459184 0.873418
105 AP5 0.457447 0.894737
106 B4P 0.457447 0.894737
107 A2D 0.456522 0.894737
108 6YZ 0.455446 0.896104
109 G G G C 0.455285 0.9125
110 ANP 0.454545 0.896104
111 5GP 5GP 0.454545 0.883117
112 ACQ 0.454545 0.896104
113 AT4 0.452632 0.884615
114 A G C C 0.451613 0.911392
115 APC G U 0.45082 0.886076
116 PRT 0.449541 0.959459
117 G U34 0.449153 0.888889
118 DG DG 0.448598 0.865854
119 ITT 0.447917 0.868421
120 BA3 0.446809 0.894737
121 35G 0.444444 0.933333
122 PCG 0.444444 0.933333
123 C2E 0.444444 0.921053
124 MGO 0.441176 0.864198
125 AN2 0.4375 0.907895
126 G C C C 0.4375 0.924051
127 NO7 0.436893 0.860759
128 M33 0.43299 0.883117
129 UCG 0.429688 0.911392
130 A G U 0.42963 0.888889
131 ACP 0.428571 0.896104
132 MGQ 0.424528 0.935897
133 7DT 0.424242 0.906667
134 APR 0.424242 0.894737
135 AR6 0.424242 0.894737
136 93A 0.42268 0.833333
137 A4P 0.420168 0.869048
138 AGS 0.42 0.873418
139 AD9 0.42 0.896104
140 G8D 0.42 0.875
141 SAP 0.42 0.873418
142 CA0 0.418367 0.896104
143 ATF 0.417476 0.884615
144 AGO 0.414634 0.888889
145 A G U U 0.414286 0.888889
146 KG4 0.414141 0.896104
147 NIA 0.413043 0.82716
148 MGV 0.412844 0.890244
149 T99 0.411765 0.884615
150 TAT 0.411765 0.884615
151 A1R 0.411215 0.839506
152 ADQ 0.411215 0.871795
153 RGT 0.410714 0.909091
154 CGP 0.409836 0.86747
155 HQG 0.409524 0.907895
156 C1Z 0.409091 0.986486
157 AMP 0.408602 0.893333
158 A 0.408602 0.893333
159 UP5 0.40678 0.873418
160 C2R 0.406593 0.906667
161 AMZ 0.406593 0.918919
162 JBT 0.405882 0.778947
163 A22 0.40566 0.907895
164 25L 0.405405 0.907895
165 ADX 0.40404 0.809524
166 8OD 0.401961 0.946667
167 4TC 0.4 0.851852
168 50T 0.4 0.883117
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1SVI; Ligand: GDP; Similar sites found with APoc: 137
This union binding pocket(no: 1) in the query (biounit: 1svi.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 1Z0A GDP None
2 1Z0A GDP None
3 1Z0A GDP None
4 1Z0F GDP None
5 2A5J GDP None
6 1Z0A GDP None
7 1Z0A GDP None
8 1Z0A GDP None
9 1OIV GDP 2.09424
10 1OIV GDP 2.09424
11 3TK1 GDP 3.07692
12 3TK1 GDP 3.07692
13 1GWN GTP 3.07692
14 5W75 GDP 3.07692
15 5W75 GDP 3.07692
16 5W75 GDP 3.07692
17 1FZQ GDP 3.31492
18 1G16 GDP 3.52941
19 1G16 GDP 3.52941
20 3QBT GNP 3.57143
21 1YRB GDP 3.58974
22 3CH5 GDP 3.58974
23 2J0V GDP 3.58974
24 2J0V GDP 3.58974
25 3GJ7 GDP 3.58974
26 2J0V GDP 3.58974
27 2J0V GDP 3.58974
28 3GJ4 GDP 3.58974
29 3GJ5 GDP 3.58974
30 3GJ7 GDP 3.58974
31 3GJ3 GDP 3.58974
32 2AWN ADP 4.10256
33 1S8F GDP 4.51977
34 1S8F GDP 4.51977
35 1S8F GDP 4.51977
36 1S8F GDP 4.51977
37 5JCZ GDP 4.61538
38 2X77 GDP 4.7619
39 2X77 GDP 4.7619
40 4HDO GNP 4.79042
41 6HDU GTP 4.8913
42 6IF2 GTP 5.12821
43 2WKQ GTP 5.64103
44 1E96 GTP 5.72917
45 1I4D GDP 5.72917
46 5KUT GDP 5.82011
47 1ZJ6 G3D 5.88235
48 1RE0 GDP 6.09756
49 2FJU GSP 6.17978
50 3Q85 GNP 6.50888
51 3Q85 GNP 6.50888
52 2EFE GNH 6.66667
53 4DKX GDP 6.66667
54 4DKX GDP 6.66667
55 3CPJ GDP 7.17949
56 3T5G GDP 7.18232
57 5O74 GDP 7.22222
58 5O74 GDP 7.22222
59 5O74 GDP 7.22222
60 5O74 GDP 7.22222
61 5O74 GDP 7.22222
62 3NKV GNP 7.42857
63 5CK5 GDP 7.69231
64 5CK5 GDP 7.69231
65 2RCN GDP 8.20513
66 2RCN GDP 8.20513
67 1VG8 GNP 8.71795
68 1VG9 GDP 9.18919
69 1VG9 GDP 9.18919
70 1VG1 GDP 9.18919
71 5W7Q GDP 9.23077
72 5W76 GDP 9.23077
73 2J59 GTP 9.52381
74 2J59 GTP 9.52381
75 3Q72 GNP 9.63855
76 3Q72 GNP 9.63855
77 3VMF GTP 9.74359
78 3WXM GTP 9.74359
79 3WXM GTP 9.74359
80 1KK1 GNP 9.74359
81 3GJ8 GDP 9.78261
82 1D2E GDP 10.2564
83 1D2E GDP 10.2564
84 1D2E GDP 10.2564
85 1D2E GDP 10.2564
86 6BC0 GSP 10.2703
87 4D0N GDP 10.2703
88 4XOI GTP 10.5556
89 5UPK GNP 10.8108
90 4YC7 GNP 11.0497
91 2CJW GDP 11.4583
92 2CJW GDP 11.4583
93 2HT6 GDP 12.6437
94 2HT6 GDP 12.6437
95 3WY9 GDP 13.1336
96 3WY9 GDP 13.1336
97 3WYA GDP 13.1336
98 2HCJ GDP 13.3333
99 3U6B GDP 13.3333
100 3U6K GDP 13.3333
101 3U6B GDP 13.3333
102 4P3Y GDP 13.3333
103 3U6K GDP 13.3333
104 4G5G GDP 13.3333
105 5JBQ GDP 13.3333
106 1D8T GDP 13.3333
107 1D8T GDP 13.3333
108 1SKQ GDP 13.3333
109 4B47 GDP 14.359
110 1DS6 GDP 15
111 2QN6 GDP 15.0538
112 1YVD GNP 15.3846
113 3CNL GNP 15.3846
114 1G7S GDP 15.8974
115 5HCN GCP 17.4359
116 3A1S GDP 21.7054
117 3A1S GDP 21.7054
118 4J0Q GDP 22.0513
119 4J0Q GDP 22.0513
120 4J0Q GDP 22.0513
121 4J0Q GDP 22.0513
122 4J0Q GDP 22.0513
123 2WJG GDP 22.3404
124 2BME GNP 24.1935
125 4NON GDP 28.2051
126 5WDR GNP 30.9942
127 5YT0 GDP 31.2821
128 5FG3 GDP 31.2821
129 2C5L GTP 35.2601
130 4DCT GDP 35.8974
131 4DCT GDP 35.8974
132 1MKY GDP 39.4872
133 5M04 GDP 41.5385
134 5TB5 GDP 42.1622
135 5TB5 GDP 42.1622
136 5E95 GDP 44.6429
137 6FA3 GNP 45.9302
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