Receptor
PDB id Resolution Class Description Source Keywords
5HPY 2.4 Å NON-ENZYME: MOBILE CRYSTAL STRUCTURE OF RHOA.GDP.MGF3-IN COMPLEX WITH HUMAN MYO RHOGAP DOMAIN HOMO SAPIENS COMPLEX RHO GTPASES RHOGAP GENE REGULATION-SIGNALING PROTCOMPLEX
Ref.: NONCANONICAL MYO9B-RHOGAP ACCELERATES RHOA GTP HYDR A DUAL-ARGININE-FINGER MECHANISM J.MOL.BIOL. V. 428 3043 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MGF F:201;
B:201;
Invalid;
Invalid;
none;
none;
submit data
81.3 F3 Mg F[Mg-...
MG B:202;
F:204;
F:203;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
GDP B:203;
F:202;
Valid;
Valid;
none;
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
5HPY 2.4 Å NON-ENZYME: MOBILE CRYSTAL STRUCTURE OF RHOA.GDP.MGF3-IN COMPLEX WITH HUMAN MYO RHOGAP DOMAIN HOMO SAPIENS COMPLEX RHO GTPASES RHOGAP GENE REGULATION-SIGNALING PROTCOMPLEX
Ref.: NONCANONICAL MYO9B-RHOGAP ACCELERATES RHOA GTP HYDR A DUAL-ARGININE-FINGER MECHANISM J.MOL.BIOL. V. 428 3043 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 65 families.
1 5HPY - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 5M70 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 5M6X - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 1OW3 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 4XSG - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
5 3LXR - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
6 3LWN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
7 3LW8 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
8 4XOI - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
9 6BCA - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
10 5IRC - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
11 5HPY - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
12 6BC0 - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
13 2GCO - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
14 1CXZ - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
15 4D0N - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 1HE1 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 5M70 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 5M6X - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 1OW3 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 2WMO - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
6 2WMN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
7 2NGR - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
8 4XSG - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
9 3LXR - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
10 3LWN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
11 3LW8 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
12 4XOI - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
13 6BCA - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
14 1E96 Kd = 2.7 uM GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
15 5IRC - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
16 5HPY - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
17 6BC0 - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
18 2GCO - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
19 1CXZ - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
20 4YC7 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
21 4D0N - 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 : 5HPY; Ligand: GDP; Similar sites found with APoc: 55
This union binding pocket(no: 1) in the query (biounit: 5hpy.bio2) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 4DCT GDP 8.10811
2 1YRB GDP 9.48276
3 3U6B GDP 10.3448
4 3U6K GDP 10.3448
5 2QN6 GDP 11.3514
6 3WY9 GDP 11.3514
7 5YT0 GDP 14.5946
8 5FG3 GDP 14.5946
9 4P3Y GDP 14.8352
10 4J0Q GDP 17.8378
11 3M1I GTP 34.5946
12 3WYF GTP 34.5946
13 3GJ4 GDP 35.1351
14 3GJ7 GDP 35.1351
15 3WYG GTP 35.1648
16 5DIF GNP 35.6757
17 5UWO GNP 35.6757
18 5UWU GNP 35.6757
19 5UWQ GNP 35.6757
20 5UWW GNP 35.6757
21 5UWP GNP 35.6757
22 4HAT GNP 35.6757
23 6CIT GNP 35.6757
24 5UWS GNP 35.6757
25 5UWT GNP 35.6757
26 5UWH GNP 35.6757
27 5DHF GNP 35.6757
28 3GJ3 GDP 35.6757
29 5BXQ GDP 35.6757
30 1WA5 GTP 37.5
31 2G77 GDP 38.9189
32 3BC1 GNP 41.6216
33 3Q72 GNP 42.1687
34 3RWO GDP 43.2432
35 1OIX GDP 44.3243
36 2A5J GDP 45.4054
37 1Z0K GTP 45.9302
38 1VG1 GDP 45.9459
39 1VG9 GDP 45.9459
40 5JCZ GDP 46.3687
41 2HT6 GDP 46.5517
42 5O74 GDP 46.6667
43 5SZH GNP 47.027
44 1S8F GDP 47.4576
45 2A9K GDP 47.5936
46 1Z0J GTP 47.6471
47 2HV8 GTP 47.6744
48 3NKV GNP 48
49 3SFV GDP 48.0663
50 4DKX GDP 48.1081
51 1D5C GDP 48.1481
52 1ZC3 GNP 48.5714
53 1UAD GNP 49.1429
54 1YVD GNP 49.7041
55 5WDR GNP 49.7076
Pocket No.: 2; Query (leader) PDB : 5HPY; Ligand: GDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5hpy.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
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