Receptor
PDB id Resolution Class Description Source Keywords
1MKY 1.9 Å NON-ENZYME: BINDING STRUCTURAL ANALYSIS OF THE DOMAIN INTERACTIONS IN DER, A SWI PROTEIN CONTAINING TWO GTPASE DOMAINS THERMOTOGA MARITIMA GTPASE ENGA DER KH-DOMAIN TANDEM G-DOMAINS LIGAND BINDIPROTEIN
Ref.: DOMAIN ARRANGEMENT OF DER, A SWITCH PROTEIN CONTAIN GTPASE DOMAINS STRUCTURE V. 10 1649 2002
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:500;
Valid;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
PO4 A:601;
A:602;
A:603;
A:604;
A:605;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
94.971 O4 P [O-]P...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1MKY 1.9 Å NON-ENZYME: BINDING STRUCTURAL ANALYSIS OF THE DOMAIN INTERACTIONS IN DER, A SWI PROTEIN CONTAINING TWO GTPASE DOMAINS THERMOTOGA MARITIMA GTPASE ENGA DER KH-DOMAIN TANDEM G-DOMAINS LIGAND BINDIPROTEIN
Ref.: DOMAIN ARRANGEMENT OF DER, A SWITCH PROTEIN CONTAIN GTPASE DOMAINS STRUCTURE V. 10 1649 2002
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 510 families.
1 1MKY - 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 391 families.
1 1MKY - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 298 families.
1 2HJG - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 4DCT Kd = 8 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 4DCS Kd = 8 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 4DCU Kd = 8 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 1MKY - 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 : 1MKY; Ligand: GDP; Similar sites found with APoc: 136
This union binding pocket(no: 1) in the query (biounit: 1mky.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 5CK5 GDP 2.8481
2 6AU6 GDP 2.91777
3 1KK1 GNP 2.92683
4 1GOT GDP 3.52941
5 1TQ4 GDP 3.87409
6 1TAD GDP 4.01235
7 1TAD ALF 4.01235
8 2RCN GDP 4.46927
9 3MD0 GDP 4.50704
10 1S8F GDP 4.51977
11 1GP2 GDP 4.81586
12 4HDO GNP 4.96894
13 4LC1 GDP 5.04451
14 5KUT GDP 5.29101
15 5HCN GCP 5.36398
16 1BH2 GSP 5.39683
17 3TK1 GDP 5.45455
18 4LPS GDP 6.19835
19 3Q72 GNP 6.62651
20 1MR3 G3D 6.62983
21 3SFV GDP 6.62983
22 4YLG GDP 6.93642
23 1S9D GDP 7.31707
24 1RE0 GDP 7.31707
25 2A5J GDP 7.32984
26 4J0Q GDP 7.3903
27 5O74 GDP 7.61421
28 1DAR GDP 7.97267
29 2WKQ GTP 8.13253
30 2C78 GNP 8.14815
31 1G16 GDP 8.23529
32 3BC1 GNP 8.47458
33 1D2E GDP 8.81612
34 2X77 GDP 9.52381
35 3AQ4 GDP 9.78261
36 1SKQ GDP 9.88506
37 3T12 GDP ALF 10.101
38 3T1O GDP 10.101
39 3WYA GDP 10.5991
40 5GOE GDP 10.9005
41 1GUA GNP 11.3772
42 5XKT GNP 11.5
43 5M04 GDP 11.6667
44 1G7S GDP 11.8451
45 1PUJ GNP 12.0567
46 5FG3 GDP 12.0729
47 5H7J GCP 12.0729
48 3N5C GDP 12.3457
49 3CNL GNP 13.7405
50 5H7K GDP 13.8539
51 5W75 GDP 14.0306
52 5W7Q GDP 14.2091
53 5TB5 GDP 14.5946
54 5TAR GDP 14.5946
55 2C5L GTP 15.0289
56 2QN6 GDP 15.0538
57 1F6B GDP 15.1515
58 5E95 GDP 15.4762
59 6BVJ GNP 15.5689
60 1WQ1 GDP 15.6627
61 6D5J GNP 16.1677
62 6D5E GNP 16.1677
63 6D5G GNP 16.1677
64 6D5H GNP 16.1677
65 6BVK GNP 16.1677
66 2HCJ GDP 16.4179
67 4D0N GDP 17.2973
68 6BC0 GSP 17.2973
69 2QTV GNP 17.3653
70 4DID GDP 17.6166
71 4R98 GNH 17.7122
72 1G7C 5GP 17.7677
73 2NGR GDP 17.801
74 1KMQ GNP 17.9348
75 2WIC GNP 17.9775
76 4B47 GDP 17.9954
77 3WYF GTP 18.2648
78 3M1I GTP 18.2648
79 4YC7 GNP 18.7845
80 5UPK GNP 18.9189
81 1YVD GNP 18.9349
82 3EC1 GDP 18.9702
83 1D8T GDP 19.084
84 3VMF GTP 19.1344
85 5W76 GDP 19.2208
86 3U6B GDP 19.5431
87 4P3Y GDP 19.5431
88 5JBQ GDP 19.5431
89 4G5G GDP 19.5431
90 3U6K GDP 19.5431
91 4PC3 GDP 19.5431
92 2BVN GNP 19.5929
93 1VG0 GDP 20.2899
94 5UWQ GNP 20.6751
95 5UWO GNP 20.6751
96 5UWS GNP 20.6751
97 2G77 GDP 20.7071
98 3GJ8 GDP 21.7195
99 3GJ3 GDP 21.7195
100 3GJ0 GDP 21.7195
101 3GJ7 GDP 21.7195
102 3GJ5 GDP 21.7195
103 3WYG GTP 21.978
104 4HAT GNP 22.2222
105 5BXQ GDP 22.2222
106 3CH5 GDP 22.2222
107 1VG1 GDP 22.7027
108 1VG9 GDP 22.7027
109 3GJ4 GDP 24.2424
110 3W5J GDP 24.5098
111 2EFE GNH 24.8619
112 3WY9 GDP 25
113 5UWU GNP 25
114 1ZJ6 G3D 26.2032
115 1FZQ GDP 26.5193
116 6G14 G4P 26.5306
117 1WA5 GTP 27.8409
118 5YT0 GDP 28.5714
119 1I4D GDP 29.1667
120 1E96 GTP 29.6875
121 2WJG GDP 31.383
122 2FJU GSP 31.4607
123 1YZG GDP 31.8436
124 4DKX GDP 32.8704
125 1Z0F GDP 32.9609
126 3DOE GTP 33.3333
127 1Z0A GDP 33.3333
128 1KSH GDP 34.4086
129 2WJH GDP 35.5422
130 3CPJ GDP 36.3229
131 1UAD GNP 37.1429
132 1DS6 GDP 38.5417
133 1SVI GDP 39.4872
134 1OIV GDP 40.3141
135 2FFQ GSP 41.5205
136 5JCZ GDP 43.0168
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