Receptor
PDB id Resolution Class Description Source Keywords
6BCA 2 Å NON-ENZYME: OTHER A COMPLEX BETWEEN PH DOMAIN OF LBCRHOGEF (AKAP-LBC) AND ACTI BOUND TO A GTP ANALOG HOMO SAPIENS RHO GTPASE GUANINE NUCLEOTIDE EXCHANGE FACTORS RHOGEF PLECKSHOMOLOGY PH DOMAIN SIGNALING PROTEIN
Ref.: CRYSTAL STRUCTURES OF THE PH DOMAINS FROM LBC FAMIL RHOGEFS BOUND TO ACTIVATED RHOA GTPASE. DATA BRIEF V. 17 356 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GSP C:202;
F:202;
Valid;
Valid;
none;
none;
submit data
539.246 C10 H16 N5 O13 P3 S c1nc2...
MG C:201;
F:201;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6BCA 2 Å NON-ENZYME: OTHER A COMPLEX BETWEEN PH DOMAIN OF LBCRHOGEF (AKAP-LBC) AND ACTI BOUND TO A GTP ANALOG HOMO SAPIENS RHO GTPASE GUANINE NUCLEOTIDE EXCHANGE FACTORS RHOGEF PLECKSHOMOLOGY PH DOMAIN SIGNALING PROTEIN
Ref.: CRYSTAL STRUCTURES OF THE PH DOMAINS FROM LBC FAMIL RHOGEFS BOUND TO ACTIVATED RHOA GTPASE. DATA BRIEF V. 17 356 2018
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 6BCA - GSP C10 H16 N5 O13 P3 S 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: GSP; Similar ligands found: 139
No: Ligand ECFP6 Tc MDL keys Tc
1 GSP 1 1
2 GP3 0.897436 0.925
3 GTP 0.853659 0.948718
4 GNH 0.829268 0.936709
5 GDP 0.817073 0.948718
6 G1R 0.8 0.936709
7 GCP 0.77907 0.925
8 GNP 0.770115 0.925
9 9GM 0.770115 0.925
10 GMV 0.767442 0.925
11 G 0.756098 0.935897
12 5GP 0.756098 0.935897
13 G2R 0.747253 0.91358
14 GDD 0.744681 0.91358
15 GDC 0.744681 0.91358
16 GKE 0.744681 0.91358
17 GPG 0.73913 0.91358
18 GTG 0.736842 0.891566
19 G3A 0.729167 0.925
20 G5P 0.721649 0.925
21 GDR 0.71875 0.91358
22 GFB 0.71875 0.91358
23 GAV 0.714286 0.987179
24 GP2 0.712644 0.91358
25 6CK 0.71134 0.891566
26 Y9Z 0.708333 0.860465
27 JB2 0.69697 0.91358
28 GKD 0.69697 0.91358
29 G2P 0.692308 0.91358
30 GDX 0.69 0.925
31 GPD 0.69 0.880952
32 ALF 5GP 0.67033 0.847059
33 0O2 0.666667 0.935897
34 YGP 0.663265 0.858824
35 JB3 0.657143 0.902439
36 GDP ALF 0.645833 0.847059
37 GDP AF3 0.645833 0.847059
38 ALF GDP 0.645833 0.847059
39 GMP 0.641975 0.835443
40 G3D 0.638298 0.935897
41 NGD 0.635514 0.91358
42 2MD 0.633027 0.894118
43 CAG 0.630631 0.840909
44 G4P 0.625 0.935897
45 FEG 0.62037 0.83908
46 U2G 0.62037 0.891566
47 G G 0.617647 0.901235
48 MGD 0.616071 0.894118
49 ZGP 0.614679 0.872093
50 CG2 0.609091 0.891566
51 TPG 0.598291 0.804348
52 3GP 0.595506 0.898734
53 GDP 7MG 0.590476 0.86747
54 GH3 0.581633 0.924051
55 PGD 0.581197 0.926829
56 MD1 0.581197 0.894118
57 2GP 0.577778 0.911392
58 GCP G 0.563107 0.875
59 DGT 0.561224 0.878049
60 DBG 0.558333 0.902439
61 G1G 0.550847 0.880952
62 AGS 0.547368 0.924051
63 SAP 0.547368 0.924051
64 FE9 0.546219 0.8
65 A G 0.543103 0.888889
66 G4M 0.539062 0.840909
67 U A G G 0.538462 0.888889
68 G A A A 0.529915 0.878049
69 MGP 0.525253 0.91358
70 GPX 0.524272 0.898734
71 BGO 0.521739 0.879518
72 DGI 0.520408 0.878049
73 6G0 0.52 0.91358
74 IDP 0.515464 0.923077
75 R7I 0.51 0.898734
76 R5I 0.51 0.898734
77 GGM 0.508475 0.858824
78 G1R G1R 0.508065 0.879518
79 PGD O 0.504 0.875
80 AKW 0.495726 0.915663
81 G U 0.491525 0.857143
82 GTA 0.486726 0.891566
83 P2G 0.484536 0.839506
84 GPC 0.483607 0.83908
85 G C 0.483333 0.857143
86 P1G 0.474747 0.829268
87 DG 0.474227 0.865854
88 DGP 0.474227 0.865854
89 BA3 0.46875 0.85
90 IMP 0.463918 0.910256
91 B4P 0.463918 0.85
92 AP5 0.463918 0.85
93 G2Q 0.462963 0.91358
94 G G G RPC 0.459016 0.833333
95 APC G U 0.456 0.843373
96 ATP 0.45 0.873418
97 HEJ 0.45 0.873418
98 G G G C 0.448819 0.869048
99 A2D 0.447917 0.85
100 5FA 0.445545 0.873418
101 AQP 0.445545 0.873418
102 A G C C 0.445312 0.86747
103 G7M 0.444444 0.901235
104 G U34 0.442623 0.847059
105 01G 0.442478 0.860465
106 ITT 0.44 0.825
107 SGP 0.44 0.876543
108 HFD 0.436893 0.831325
109 G C C C 0.431818 0.879518
110 AT4 0.43 0.911392
111 AN2 0.43 0.8625
112 DG DG 0.428571 0.825581
113 A4P 0.42623 0.829545
114 UCG 0.424242 0.86747
115 PCG 0.423077 0.886076
116 C2E 0.423077 0.875
117 35G 0.423077 0.886076
118 MGO 0.420561 0.823529
119 ADP 0.42 0.873418
120 ANP 0.419048 0.851852
121 5GP 5GP 0.419048 0.839506
122 ADQ 0.418182 0.829268
123 7DT 0.417476 0.860759
124 AR6 0.417476 0.85
125 APR 0.417476 0.85
126 PRT 0.417391 0.910256
127 C1Z 0.415929 0.935897
128 A G U 0.414286 0.847059
129 AD9 0.413462 0.851852
130 UP5 0.413223 0.831325
131 A22 0.412844 0.8625
132 25L 0.412281 0.8625
133 M33 0.411765 0.839506
134 JBT 0.410405 0.783505
135 ACP 0.407767 0.851852
136 6YZ 0.407407 0.851852
137 ACQ 0.40566 0.851852
138 A1R 0.405405 0.8
139 A G U U 0.4 0.847059
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6BCA; Ligand: GSP; Similar sites found with APoc: 71
This union binding pocket(no: 1) in the query (biounit: 6bca.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 2FH5 GTP 7.28477
2 4RD0 GDP 8.10811
3 4DCT GDP 8.10811
4 2BVN GNP 8.60927
5 2C78 GNP 11.2583
6 3WXM GTP 12.5828
7 2XTZ GSP 13.5135
8 5FG3 GDP 14.5946
9 1YRB GDP 16.7568
10 1BH2 GSP 16.7568
11 2ODE ALF GDP 16.7568
12 1TAD ALF 18.3784
13 1TAD GDP 18.3784
14 3CX8 GSP 18.543
15 1CS4 GSP 20.5405
16 4M9Q GNP 22.5166
17 4NCN GTP 23.7838
18 1KSH GDP 28.1081
19 1R4A GNP 31.3725
20 1FQJ ALF 32.973
21 3M1I GTP 34.0541
22 5XC5 GTP 34.0909
23 1J2J GTP 34.3373
24 1O3Y GTP 34.3373
25 3GJ7 GDP 34.5946
26 3GJ4 GDP 34.5946
27 3GJ5 GDP 34.5946
28 5DIF GNP 35.1351
29 5UWP GNP 35.1351
30 5UWI GNP 35.1351
31 5UWQ GNP 35.1351
32 5UWW GNP 35.1351
33 5UWR GNP 35.1351
34 5DHF GNP 35.1351
35 5UWU GNP 35.1351
36 5UWO GNP 35.1351
37 4HAT GNP 35.1351
38 6CIT GNP 35.1351
39 5UWS GNP 35.1351
40 5UWT GNP 35.1351
41 5UWH GNP 35.1351
42 5UWJ GNP 35.1351
43 1IBR GNP 35.1351
44 5DI9 GNP 35.1351
45 5BXQ GDP 35.1351
46 1WA5 GTP 36.9318
47 1Z06 GNP 40
48 3BC1 GNP 42.1622
49 3Q72 GNP 42.7711
50 1YZN GNP 43.7838
51 2BME GNP 43.7838
52 1OIX GDP 44.8649
53 1X1R GDP 45.5056
54 1VG1 GDP 46.4865
55 1VG8 GNP 46.4865
56 1VG0 GDP 46.4865
57 1Z0K GTP 46.5116
58 5O74 GDP 47.2222
59 5OCG GNP 47.5676
60 1EK0 GNP 47.6471
61 1S8F GDP 48.0226
62 5TB5 GDP 48.1081
63 2HV8 GTP 48.2558
64 1TU3 GNP 48.538
65 4C4P GNP 48.5549
66 3MJH GTP 48.8095
67 1R2Q GNP 48.8235
68 1Z0A GDP 48.8506
69 1YVD GNP 49.1124
70 1ZC3 GNP 49.1429
71 1YZQ GNP 49.4118
Pocket No.: 2; Query (leader) PDB : 6BCA; Ligand: GSP; 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: 6bca.bio2) has 23 residues
No: Leader PDB Ligand Sequence Similarity
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