Receptor
PDB id Resolution Class Description Source Keywords
3SFV 1.73 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE GDP-BOUND RAB1A S25N MUTANT IN COMP THE COILED-COIL DOMAIN OF LIDA FROM LEGIONELLA PNEUMOPHILA HOMO SAPIENS LIDA-RAB COMPLEX COILED-COIL DOMAIN TYPE IV EFFECTOR PROTELEGIONELLA GDP BINDING PROTEIN TRANSPORT-PROTEIN BINDING
Ref.: STRUCTURAL INSIGHTS INTO A UNIQUE LEGIONELLA PNEUMO EFFECTOR LIDA RECOGNIZING BOTH GDP AND GTP BOUND RA THEIR ACTIVE STATE PLOS PATHOG. V. 8 02528 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:200;
 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
3SFV 1.73 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE GDP-BOUND RAB1A S25N MUTANT IN COMP THE COILED-COIL DOMAIN OF LIDA FROM LEGIONELLA PNEUMOPHILA HOMO SAPIENS LIDA-RAB COMPLEX COILED-COIL DOMAIN TYPE IV EFFECTOR PROTELEGIONELLA GDP BINDING PROTEIN TRANSPORT-PROTEIN BINDING
Ref.: STRUCTURAL INSIGHTS INTO A UNIQUE LEGIONELLA PNEUMO EFFECTOR LIDA RECOGNIZING BOTH GDP AND GTP BOUND RA THEIR ACTIVE STATE PLOS PATHOG. V. 8 02528 2012
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 3SFV - 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 1331 families.
1 3TNF - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
2 3SFV - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (81)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 223 families.
1 3QBT - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
2 5WFO - 5UU C19 H16 Cl F N2 c1cc(ccc1N....
3 6T5U - MKW C25 H24 Cl N5 O2 CCC(=O)N1C....
4 5WHA - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 6EPO - BPW C9 H12 Cl N c1cc(ccc1C....
6 6OB3 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
7 6FA3 Kd = 0.038 uM D1Z C30 H36 N4 O5 CN(C)Cc1cc....
8 6WGN - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
9 5WFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
10 5E95 Kd = 15.7 nM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
11 6FA4 Kd = 0.051 uM D1W C23 H25 N3 O3 CN(C)Cc1cc....
12 5O2T Kd = 3.9 nM GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
13 6H46 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
14 1WQ1 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
15 3KUD - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
16 6EPP - BOQ C12 H19 N O3 CCOC(=O)c1....
17 5WPM - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
18 1LFD - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
19 5WFR - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
20 5UFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
21 6AMB - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
22 6EPN - BQ2 C11 H13 N O2 c1ccc2c(c1....
23 6FA1 - D2Z C20 H25 N2 O4 C[NH+](C)C....
24 6GQX - F8K C23 H27 N2 O2 C[NH+](C)C....
25 5UFE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
26 6EPM - BQ5 C13 H15 N3 c1ccc(cc1)....
27 5WFP - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
28 5WHB - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
29 5WPL - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
30 5XCO - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
31 1NVU - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
32 5WHE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
33 3KUC - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
34 1C1Y - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
35 5TAR - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
36 4DXA - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
37 4HDO - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
38 3MJH - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
39 3CF6 - SP1 C10 H12 N5 O5 P S c1nc(c2c(n....
40 5JCZ - GDP BEF n/a n/a
41 1Z0K - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
42 2CJW Kd = 2.5 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
43 2C5L - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
44 4K81 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
45 4KVG - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
46 3TNF - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
47 5Z2M - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
48 1ZC4 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
49 1ZC3 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
50 2A9K - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
51 2A78 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
52 2HV8 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
53 4C4P - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
54 2GZD - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
55 2GZH - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
56 1VG0 Kd = 0.8 nM GER C20 H34 CC=C(/C)CC....
57 1VG9 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
58 3T5G - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
59 6RIR Kd = 3.3 uM GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
60 6IYB - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
61 3TKL - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
62 4D0G - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
63 3DDC - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
64 2EFE - GNH C10 H16 N6 O10 P2 c1nc2c(n1[....
65 4G01 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
66 2EFC - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
67 2EFH - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
68 6ZSJ Kd = 0.24 uM GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
69 6ZSI Kd = 0.29 uM GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
70 5SZH - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
71 6ZRN - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
72 6ZQT - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
73 1TU3 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
74 2D7C - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
75 1UAD Ka = 7260000 M^-1 GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
76 5O74 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
77 4LX0 - BEF GDP n/a n/a
78 3SFV - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
79 4URZ Kd = 3 mM VJP C11 H14 N2 O3 S c1cc(ccc1N....
80 4URX Kd = 1.3 mM HXY C11 H14 Br N c1cc(ccc1C....
81 4URY Kd = 6 mM RV1 C10 H12 N2 O3 S c1cc(ccc1N....
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 : 3SFV; Ligand: GDP; Similar sites found with APoc: 66
This union binding pocket(no: 1) in the query (biounit: 3sfv.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 4LC1 GDP 2.67062
2 4LC1 GDP 2.67062
3 2AWN ADP 3.48837
4 2AWN ADP 3.48837
5 2AWN ADP 3.48837
6 2AWN ADP 3.48837
7 5M04 GDP 4.65116
8 2RCN GDP 5.52486
9 1MKY GDP 6.62983
10 4NON GDP 6.62983
11 2WJG GDP 6.62983
12 1SKQ GDP 6.62983
13 2WJG GDP 6.62983
14 3MD0 GDP 8.28729
15 2HCJ GDP 8.83978
16 1D8T GDP 8.83978
17 1GOJ ADP 9.94475
18 5CK5 GDP 11.0497
19 5CK5 GDP 11.0497
20 5CK5 GDP 11.0497
21 5CK5 GDP 11.0497
22 4DCT GDP 12.2093
23 4DCT GDP 12.2093
24 5HCN GCP 13.0268
25 2VVG ADP 14.9171
26 2VVG ADP 14.9171
27 3EC1 GDP 16.0221
28 5YT0 GDP 23.2044
29 4B47 GDP 23.2044
30 5FG3 GDP 23.2044
31 1YRB GDP 24.3094
32 1YRB GDP 24.3094
33 3PQC GDP 27.0718
34 5KUT GDP 32.5967
35 5KUT GDP 32.5967
36 1ZD9 GDP 33.7017
37 1ZJ6 G3D 33.7017
38 1ZJ6 G3D 33.7017
39 1KK1 GNP 34.2541
40 1DS6 GDP 34.8066
41 1YZG GDP 35.1955
42 1MR3 G3D 37.0166
43 1FZQ GDP 37.5691
44 1RE0 GDP 42.0732
45 3SBD GNP 43.6464
46 5UPK GNP 44.1989
47 1GRN GDP 44.7514
48 2QN6 GDP 45.1613
49 1E96 GTP 45.3039
50 3Q85 GNP 45.5621
51 3Q85 GNP 45.5621
52 1I4D GDP 45.8564
53 1RYH GNP 46.4088
54 3Q72 GNP 47.5904
55 5HPY GDP 48.0663
56 5BXQ GDP 48.6188
57 5BXQ GDP 48.6188
58 5BXQ GDP 48.6188
59 3CH5 GDP 48.6188
60 2J0V GDP 48.6188
61 2J0V GDP 48.6188
62 4HAT GNP 48.6188
63 6X2U GNP 48.6188
64 6X2Y GNP 48.6188
65 3M1I GTP 48.6188
66 2HT6 GDP 49.4253
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