Receptor
PDB id Resolution Class Description Source Keywords
3A1S 1.5 Å NON-ENZYME: TRANSPORT CRYSTAL STRUCTUE OF THE CYTOSOLIC DOMAIN OF T. MARITIMA FEOB IRON IRANSPORTER IN GDP FORM I THERMOTOGA MARITIMA FEOB IRON TRANSPORTER SMALL GTPASE G PROTEIN GDI TRANSPORT PROTEIN
Ref.: STRUCTURAL BASIS OF NOVEL INTERACTIONS BETWEEN THE SMALL-GTPASE AND GDI-LIKE DOMAINS IN PROKARYOTIC FEOB IRON TRANSPORTER STRUCTURE V. 17 1345 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:1;
B:2;
Valid;
Valid;
none;
none;
Kd = 14.8 uM
443.201 C10 H15 N5 O11 P2 c1nc2...
MG A:3;
A:4;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
MPD A:6;
B:7;
Invalid;
Invalid;
none;
none;
submit data
118.174 C6 H14 O2 C[C@@...
MRD A:5;
Invalid;
none;
submit data
118.174 C6 H14 O2 C[C@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3A1S 1.5 Å NON-ENZYME: TRANSPORT CRYSTAL STRUCTUE OF THE CYTOSOLIC DOMAIN OF T. MARITIMA FEOB IRON IRANSPORTER IN GDP FORM I THERMOTOGA MARITIMA FEOB IRON TRANSPORTER SMALL GTPASE G PROTEIN GDI TRANSPORT PROTEIN
Ref.: STRUCTURAL BASIS OF NOVEL INTERACTIONS BETWEEN THE SMALL-GTPASE AND GDI-LIKE DOMAINS IN PROKARYOTIC FEOB IRON TRANSPORTER STRUCTURE V. 17 1345 2009
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 220 families.
1 3A1S Kd = 14.8 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 3A1U - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
3 3A1T Kd = 14.8 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 186 families.
1 3A1S Kd = 14.8 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 3A1U - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
3 3A1T Kd = 14.8 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 157 families.
1 3B1V - GGM C18 H24 N7 O14 P3 CNc1ccccc1....
2 4NON Kd = 5.71 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 3B1W - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 3B1Y - GNH C10 H16 N6 O10 P2 c1nc2c(n1[....
5 3TAH - BGO C18 H22 N6 O12 P2 CNc1ccccc1....
6 3LX5 - AGO C18 H22 N7 O14 P3 CNc1ccccc1....
7 2WIC - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
8 4R98 - GNH C10 H16 N6 O10 P2 c1nc2c(n1[....
9 3A1S Kd = 14.8 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
10 3A1U - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
11 3A1T Kd = 14.8 uM 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 : 3A1S; Ligand: GDP; Similar sites found with APoc: 22
This union binding pocket(no: 1) in the query (biounit: 3a1s.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 1TQ4 GDP 3.10078
2 1ZC3 GNP 4.57143
3 1UAD GNP 4.57143
4 4LHW GNP 4.5977
5 6J72 GTP 5.03876
6 6FF8 GTP 6.07735
7 6FF8 GTP 6.07735
8 1I4D GDP 13.8393
9 6BSX GDP 17.9775
10 6BSX E7S 17.9775
11 6BSX E7S 17.9775
12 1SVI GDP 21.7054
13 4DCT GDP 29.0698
14 1TU3 GNP 29.1139
15 1TU3 GNP 29.1139
16 1TU3 GNP 29.1139
17 1TU3 GNP 29.1139
18 5O2T GSP 38.4615
19 3PQC GDP 41.0256
20 3PQC GDP 41.0256
21 1CLU DBG 44.5783
22 5E95 GDP 44.6429
Pocket No.: 2; Query (leader) PDB : 3A1S; Ligand: GDP; Similar sites found with APoc: 44
This union binding pocket(no: 2) in the query (biounit: 3a1s.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 5KUT GDP None
2 3SBD GNP 2.6738
3 1TQ4 GDP 3.10078
4 2WKQ GTP 3.48837
5 2FJU GSP 3.87597
6 1UAD GNP 4.57143
7 4LHW GNP 4.5977
8 4LHW GNP 4.5977
9 3QBT GNP 4.5977
10 5YT0 GDP 4.65116
11 1U8Z GDP 4.7619
12 6FF8 GTP 6.07735
13 3MJH GTP 7.14286
14 2BME GNP 8.06452
15 2BME GNP 8.06452
16 6HDU GTP 9.78261
17 6HDU GTP 9.78261
18 1E96 GTP 10.3448
19 5UPK GNP 11.2403
20 3BC1 GNP 11.8644
21 3WYA GDP 11.9816
22 1I4D GDP 13.8393
23 5O74 GDP 13.8889
24 5O74 GDP 13.8889
25 5O74 GDP 13.8889
26 3NKV GNP 14.2857
27 6G14 G4P 15.8915
28 1MKY GDP 16.6667
29 6BSX GDP 17.9775
30 6BSX E7S 17.9775
31 5FG3 GDP 18.6047
32 1SVI GDP 21.7054
33 3Q85 GNP 28.4024
34 4DCT GDP 29.0698
35 1TU3 GNP 29.1139
36 1TU3 GNP 29.1139
37 1TU3 GNP 29.1139
38 2X77 GDP 35.9788
39 6FA3 GNP 37.7907
40 3PQC GDP 41.0256
41 3PQC GDP 41.0256
42 4K81 GTP 43.8596
43 1CLU DBG 44.5783
44 5E95 GDP 44.6429
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