Receptor
PDB id Resolution Class Description Source Keywords
2RHO 2.45 Å NON-ENZYME: CELL_CYCLE SYNTHETIC GENE ENCODED BACILLUS SUBTILIS FTSZ NCS DIMER WITH BOUND GDP AND GTP-GAMMA-S BACILLUS SUBTILIS CELL DIVISION PROTEIN TUBULIN HOMOLOG GTP-BINDING POLYMERIZATION GTPASE CELL CYCLE STRUCTURAL GENOMICS PSI-2 PROTEIN STRUCTURE INITIATIVE ACCELERATED TECHNOLOGIES CENTER FOR GENE TO 3D STRUCTURE ATCG3D
Ref.: COMBINED PROTEIN CONSTRUCT AND SYNTHETIC GENE ENGINEERING FOR HETEROLOGOUS PROTEIN EXPRESSION AND CRYSTALLIZATION USING GENE COMPOSER. BMC BIOTECHNOL. V. 9 37 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP B:501;
Valid;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
GSP A:501;
Valid;
none;
submit data
539.246 C10 H16 N5 O13 P3 S c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2RHO 2.45 Å NON-ENZYME: CELL_CYCLE SYNTHETIC GENE ENCODED BACILLUS SUBTILIS FTSZ NCS DIMER WITH BOUND GDP AND GTP-GAMMA-S BACILLUS SUBTILIS CELL DIVISION PROTEIN TUBULIN HOMOLOG GTP-BINDING POLYMERIZATION GTPASE CELL CYCLE STRUCTURAL GENOMICS PSI-2 PROTEIN STRUCTURE INITIATIVE ACCELERATED TECHNOLOGIES CENTER FOR GENE TO 3D STRUCTURE ATCG3D
Ref.: COMBINED PROTEIN CONSTRUCT AND SYNTHETIC GENE ENGINEERING FOR HETEROLOGOUS PROTEIN EXPRESSION AND CRYSTALLIZATION USING GENE COMPOSER. BMC BIOTECHNOL. V. 9 37 2009
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 24 families.
1 2RHL - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 2RHO - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
70% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 4DXD - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 3WGM - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
3 2RHL - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 2RHO - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
5 5XDV - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
6 5XDT - MB3 C5 H9 N O CN1CCCC1=O
7 5H5G - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
8 5H5H - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 5H5I - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
10 5XDW - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
11 5MN4 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
12 5XDU - 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 13 families.
1 4DXD - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 3WGM - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
3 2RHL - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 2RHO - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
5 5XDV - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
6 5XDT - MB3 C5 H9 N O CN1CCCC1=O
7 5H5G - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
8 5H5H - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 5H5I - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
10 5XDW - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
11 5MN4 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
12 5XDU - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
13 1W5F - G2P C11 H18 N5 O13 P3 c1nc2c(n1[....
14 1RQ2 ic50 = 3 mM CIT C6 H8 O7 C(C(=O)O)C....
15 1RLU - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
16 1W5B - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
17 1W5A - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
18 1W58 - G2P C11 H18 N5 O13 P3 c1nc2c(n1[....
19 2VAP - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
20 2R6R - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
21 2R75 Kd = 714 nM 01G C14 H23 N6 O15 P3 C1COCCN1c2....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GDP; Similar ligands found: 153
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 G 0.828947 0.986486
7 5GP 0.828947 0.986486
8 G1R 0.82716 0.986667
9 GCP 0.82716 0.973684
10 GSP 0.817073 0.948718
11 GAV 0.797619 0.961039
12 GMV 0.792683 0.973684
13 G2P 0.77381 0.961039
14 G2R 0.770115 0.961039
15 GDP MG 0.759036 0.923077
16 GP2 0.756098 0.961039
17 GDP BEF 0.75 0.9
18 GDD 0.747253 0.961039
19 GKE 0.747253 0.961039
20 GDC 0.747253 0.961039
21 GPG 0.741573 0.961039
22 G3D 0.732558 0.986486
23 ALF 5GP 0.729412 0.888889
24 Y9Z 0.728261 0.902439
25 GTP MG 0.724138 0.923077
26 BEF GDP 0.724138 0.888889
27 G5P 0.723404 0.973684
28 GFB 0.72043 0.961039
29 GTG 0.72043 0.936709
30 GDR 0.72043 0.961039
31 G4P 0.715909 0.986486
32 GCP G 0.715909 0.935065
33 6CK 0.712766 0.936709
34 G3A 0.712766 0.973684
35 GDP ALF 0.7 0.888889
36 GDP AF3 0.7 0.888889
37 YGP 0.698925 0.901235
38 JB2 0.697917 0.961039
39 GKD 0.697917 0.961039
40 GDX 0.690722 0.973684
41 GPD 0.690722 0.925
42 GMP 0.684211 0.88
43 0O2 0.666667 0.986486
44 G G 0.659574 0.935065
45 JB3 0.656863 0.948718
46 NGD 0.650485 0.961039
47 GDP 7MG 0.636364 0.911392
48 DGI 0.636364 0.923077
49 U2G 0.634615 0.936709
50 GPX 0.634409 0.946667
51 IDP 0.632184 0.972973
52 2MD 0.632075 0.891566
53 CAG 0.62963 0.880952
54 CG2 0.622642 0.936709
55 FEG 0.619048 0.879518
56 MGD 0.614679 0.891566
57 ZGP 0.613208 0.869048
58 GH3 0.612903 0.973333
59 3GP 0.611765 0.946667
60 MD1 0.607143 0.891566
61 PGD 0.59292 0.925
62 DGT 0.591398 0.923077
63 BGO 0.588785 0.924051
64 TPG 0.582609 0.840909
65 DBG 0.582609 0.948718
66 2GP 0.574713 0.96
67 FE9 0.570175 0.776596
68 I2C FE2 CMO CMO 0.566372 0.808989
69 G A A A 0.553571 0.923077
70 MGP 0.553191 0.961039
71 U A G G 0.548673 0.935065
72 G4M 0.548387 0.880952
73 6G0 0.547368 0.961039
74 G1R G1R 0.542373 0.924051
75 P2G 0.527473 0.883117
76 PGD O 0.525 0.850575
77 ADP 0.522222 0.92
78 GGM 0.517544 0.901235
79 DG 0.516484 0.910256
80 DGP 0.516484 0.910256
81 P1G 0.516129 0.871795
82 G G U 0.509259 0.935065
83 G1G 0.508475 0.925
84 IMP 0.505495 0.959459
85 G C 0.504348 0.9
86 GPC 0.491525 0.879518
87 G7M 0.483871 0.948052
88 6AD 0.479592 0.841463
89 ATP 0.473684 0.92
90 G2Q 0.471154 0.961039
91 U G A 0.469697 0.888889
92 5FA 0.46875 0.92
93 AQP 0.46875 0.92
94 GTA 0.468468 0.936709
95 7DD 0.468085 0.906667
96 G G G RPC 0.466102 0.875
97 SGP 0.463158 0.82716
98 01G 0.462963 0.902439
99 B4P 0.457447 0.894737
100 AP5 0.457447 0.894737
101 A2D 0.456522 0.894737
102 G G G C 0.455285 0.9125
103 ACQ 0.454545 0.896104
104 5GP 5GP 0.454545 0.883117
105 ANP 0.454545 0.896104
106 A G C C 0.451613 0.911392
107 APC G U 0.45082 0.886076
108 G U34 0.449153 0.888889
109 DG DG 0.448598 0.865854
110 ITT 0.447917 0.868421
111 BA3 0.446809 0.894737
112 35G 0.444444 0.933333
113 C2E 0.444444 0.921053
114 PCG 0.444444 0.933333
115 MGO 0.441176 0.864198
116 AN2 0.4375 0.907895
117 G C C C 0.4375 0.924051
118 M33 0.43299 0.883117
119 UCG 0.429688 0.911392
120 A G U 0.42963 0.888889
121 ACP 0.428571 0.896104
122 MGQ 0.424528 0.935897
123 7DT 0.424242 0.906667
124 APR 0.424242 0.894737
125 AR6 0.424242 0.894737
126 93A 0.42268 0.833333
127 A4P 0.420168 0.869048
128 SAP 0.42 0.873418
129 AD9 0.42 0.896104
130 AGS 0.42 0.873418
131 G8D 0.42 0.875
132 CA0 0.418367 0.896104
133 ATF 0.417476 0.884615
134 AGO 0.414634 0.888889
135 NIA 0.413043 0.82716
136 MGV 0.412844 0.890244
137 TAT 0.411765 0.884615
138 A1R 0.411215 0.839506
139 ADQ 0.411215 0.871795
140 RGT 0.410714 0.909091
141 CGP 0.409836 0.86747
142 AMP 0.408602 0.893333
143 A 0.408602 0.893333
144 UP5 0.40678 0.873418
145 C2R 0.406593 0.906667
146 AMZ 0.406593 0.918919
147 JBT 0.405882 0.778947
148 A22 0.40566 0.907895
149 25L 0.405405 0.907895
150 ADX 0.40404 0.809524
151 8OD 0.401961 0.946667
152 4TC 0.4 0.851852
153 50T 0.4 0.883117
Ligand no: 2; Ligand: GSP; Similar ligands found: 132
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 GMV 0.767442 0.925
10 5GP 0.756098 0.935897
11 G 0.756098 0.935897
12 G2R 0.747253 0.91358
13 GKE 0.744681 0.91358
14 GDD 0.744681 0.91358
15 GDC 0.744681 0.91358
16 GPG 0.73913 0.91358
17 GTG 0.736842 0.891566
18 G3A 0.729167 0.925
19 G5P 0.721649 0.925
20 GDR 0.71875 0.91358
21 GFB 0.71875 0.91358
22 GAV 0.714286 0.987179
23 GP2 0.712644 0.91358
24 6CK 0.71134 0.891566
25 Y9Z 0.708333 0.860465
26 JB2 0.69697 0.91358
27 GKD 0.69697 0.91358
28 GDP MG 0.696629 0.878049
29 G2P 0.692308 0.91358
30 GDX 0.69 0.925
31 GPD 0.69 0.880952
32 GDP BEF 0.688889 0.857143
33 GCP G 0.677419 0.888889
34 ALF 5GP 0.67033 0.847059
35 0O2 0.666667 0.935897
36 GTP MG 0.666667 0.878049
37 BEF GDP 0.666667 0.847059
38 YGP 0.663265 0.858824
39 JB3 0.657143 0.902439
40 GDP ALF 0.645833 0.847059
41 GDP AF3 0.645833 0.847059
42 G G 0.642857 0.888889
43 GMP 0.641975 0.835443
44 G3D 0.638298 0.935897
45 NGD 0.635514 0.91358
46 2MD 0.633027 0.894118
47 CAG 0.630631 0.840909
48 G4P 0.625 0.935897
49 U2G 0.62037 0.891566
50 FEG 0.62037 0.83908
51 MGD 0.616071 0.894118
52 ZGP 0.614679 0.872093
53 CG2 0.609091 0.891566
54 TPG 0.598291 0.804348
55 3GP 0.595506 0.898734
56 GDP 7MG 0.590476 0.86747
57 GH3 0.581633 0.924051
58 MD1 0.581197 0.894118
59 PGD 0.581197 0.926829
60 2GP 0.577778 0.911392
61 DGT 0.561224 0.878049
62 DBG 0.558333 0.902439
63 G1G 0.550847 0.880952
64 SAP 0.547368 0.924051
65 AGS 0.547368 0.924051
66 FE9 0.546219 0.8
67 G4M 0.539062 0.840909
68 U A G G 0.538462 0.888889
69 G A A A 0.529915 0.878049
70 MGP 0.525253 0.91358
71 GPX 0.524272 0.898734
72 BGO 0.521739 0.879518
73 DGI 0.520408 0.878049
74 6G0 0.52 0.91358
75 I2C FE2 CMO CMO 0.516667 0.774194
76 IDP 0.515464 0.923077
77 GGM 0.508475 0.858824
78 G1R G1R 0.508065 0.879518
79 PGD O 0.504 0.875
80 G G U 0.5 0.888889
81 GTA 0.486726 0.891566
82 P2G 0.484536 0.839506
83 GPC 0.483607 0.83908
84 G C 0.483333 0.857143
85 P1G 0.474747 0.829268
86 DG 0.474227 0.865854
87 DGP 0.474227 0.865854
88 BA3 0.46875 0.85
89 AP5 0.463918 0.85
90 B4P 0.463918 0.85
91 IMP 0.463918 0.910256
92 G2Q 0.462963 0.91358
93 G G G RPC 0.459016 0.833333
94 APC G U 0.456 0.843373
95 U G A 0.452555 0.847059
96 ATP 0.45 0.873418
97 G G G C 0.448819 0.869048
98 A2D 0.447917 0.85
99 5FA 0.445545 0.873418
100 AQP 0.445545 0.873418
101 A G C C 0.445312 0.86747
102 G7M 0.444444 0.901235
103 G U34 0.442623 0.847059
104 01G 0.442478 0.860465
105 ITT 0.44 0.825
106 SGP 0.44 0.876543
107 G C C C 0.431818 0.879518
108 AN2 0.43 0.8625
109 DG DG 0.428571 0.825581
110 A4P 0.42623 0.829545
111 UCG 0.424242 0.86747
112 C2E 0.423077 0.875
113 PCG 0.423077 0.886076
114 35G 0.423077 0.886076
115 MGO 0.420561 0.823529
116 ADP 0.42 0.873418
117 ANP 0.419048 0.851852
118 5GP 5GP 0.419048 0.839506
119 ADQ 0.418182 0.829268
120 APR 0.417476 0.85
121 AR6 0.417476 0.85
122 7DT 0.417476 0.860759
123 A G U 0.414286 0.847059
124 AD9 0.413462 0.851852
125 UP5 0.413223 0.831325
126 A22 0.412844 0.8625
127 25L 0.412281 0.8625
128 M33 0.411765 0.839506
129 JBT 0.410405 0.783505
130 ACP 0.407767 0.851852
131 ACQ 0.40566 0.851852
132 A1R 0.405405 0.8
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2RHO; Ligand: GSP; Similar sites found: 64
This union binding pocket(no: 1) in the query (biounit: 2rho.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3UW4 MAA CHG PRO 0DQ 0.005546 0.44488 None
2 4NAE 1GP 0.02179 0.41252 None
3 4WG0 CHD 0.03463 0.40008 None
4 2VSL MAA LYS PRO PHE 0.01582 0.41445 0.615385
5 1R55 097 0.01648 0.41354 1.40187
6 3M89 GSP 0.0000004828 0.62442 1.84615
7 1J78 OLA 0.01525 0.41057 1.84615
8 4MXP DB4 0.01457 0.40452 1.84615
9 2CJZ PTR 0.007405 0.43239 1.96721
10 2GMP NAG MAN 0.04209 0.40056 2.38095
11 3CM2 X23 0.00986 0.42959 2.46154
12 2R0D 4IP 0.01477 0.41598 2.46154
13 2R09 4IP 0.01668 0.41328 2.46154
14 3ZPG 5GP 0.02099 0.41302 2.46154
15 4IA6 EIC 0.02627 0.4099 2.46154
16 4GK9 MAN BMA MAN MAN MAN 0.0311 0.40056 2.86738
17 5EFC GTP 0.03377 0.40237 2.87356
18 2HK9 ATR 0.01799 0.40755 3.38462
19 5EXA 5SO 0.02677 0.40276 3.38462
20 4XW2 SIM 0.008179 0.4035 3.53535
21 2X2T GAL NGA 0.009802 0.42446 3.92157
22 4ZNO SUC 0.01779 0.42934 4
23 5A1S FLC 0.02736 0.40662 4
24 1M0S CIT 0.008686 0.42772 4.10959
25 2X1L MET 0.01016 0.42673 4.30769
26 5EYP GTP 0.00000006767 0.57327 4.61538
27 5EYP GDP 0.00000007209 0.56359 4.61538
28 5EIB GTP 0.0000001991 0.55573 4.61538
29 4LNU GTP 0.0000002371 0.55293 4.61538
30 4LNU GDP 0.000003972 0.53425 4.61538
31 1YXM ADE 0.01389 0.41158 4.9505
32 5M6N 7H9 0.005858 0.44139 5.08475
33 5C83 4YN 0.006305 0.4348 5.45455
34 5ITZ GTP 0.0000004015 0.54438 5.51181
35 5ITZ GDP 0.000002002 0.54094 5.51181
36 5M6M 7H8 0.008262 0.42883 5.51181
37 3ZJQ NCA 0.0288 0.40783 5.53846
38 4D86 ADP 0.00102 0.44166 5.54217
39 1VI2 NAD 0.00584 0.40256 5.66667
40 4QAG F95 0.01796 0.4247 5.84615
41 5KUT GDP 0.01555 0.40683 6.34921
42 1YP1 LYS ASN LEU 0.01388 0.42183 6.43564
43 3CB2 GDP 0.000002423 0.56827 6.46154
44 2H88 TEO 0.02034 0.40887 6.79612
45 5AOA PPI 0.003285 0.44102 6.99301
46 4JZ8 CIT 0.01354 0.4245 7.25552
47 2BOS GLA GAL GLC NBU 0.01391 0.427 7.35294
48 2CHN NGT 0.01218 0.40821 7.38462
49 5IRC GDP 0.01462 0.40445 7.52688
50 4Z7X 3CX 0.02364 0.40589 7.56302
51 3RYC GTP 0.00000006548 0.54051 7.69231
52 3RYC GDP 0.000004675 0.52074 7.69231
53 1BRW URA 0.0305 0.4039 7.69231
54 4B9E FAH 0.02108 0.41241 8.63787
55 5X2N ALA 0.03515 0.40275 8.92308
56 2BTO GTP 0.000000003231 0.6472 10.1852
57 2RI1 GLP 0.03416 0.40222 10.6383
58 4UP4 NDG 0.03452 0.41009 11.3846
59 2UZH IPE 0.03273 0.40283 11.5152
60 4V15 PLP 0.02045 0.40105 14.1538
61 3ZBQ GDP 0.000008125 0.53243 14.4615
62 4TR1 GSH 0.03046 0.40388 15.2174
63 5TVF PUT 0.03302 0.40003 17.6471
64 4EI7 GDP 0.0000002112 0.58076 35.6923
Pocket No.: 2; Query (leader) PDB : 2RHO; Ligand: GDP; Similar sites found: 26
This union binding pocket(no: 2) in the query (biounit: 2rho.bio2) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1R55 097 0.006071 0.42075 1.40187
2 3M89 GSP 0.000000126 0.62777 1.84615
3 4IA6 EIC 0.009609 0.42021 2.46154
4 3UCJ AZM 0.00929 0.41175 2.64317
5 3L1N PLM 0.0195 0.40029 3.60825
6 4LNU GDP 0.000001676 0.49758 4.61538
7 5EYP GDP 0.00000357 0.44881 4.61538
8 5EIB GTP 0.000007502 0.44724 4.61538
9 4LNU GTP 0.000008487 0.44591 4.61538
10 5EYP GTP 0.00001293 0.43907 4.61538
11 2P9H IPT 0.009379 0.40715 4.83271
12 1UYY BGC BGC 0.01213 0.41065 5.34351
13 5ITZ GDP 0.000002939 0.48204 5.51181
14 5ITZ GTP 0.00001029 0.4415 5.51181
15 4D86 ADP 0.000816 0.42155 5.54217
16 1WHT BZS 0.01386 0.41234 6.15385
17 3CB2 GDP 0.000004937 0.52079 6.46154
18 4JZ8 CIT 0.009786 0.4175 7.25552
19 3RYC GDP 0.000002342 0.47722 7.69231
20 3RYC GTP 0.000005204 0.42848 7.69231
21 1XHL NDP 0.02107 0.4058 9.42761
22 2BTO GTP 0.0000005551 0.49939 10.1852
23 3SJH ATP 0.01444 0.40001 11.1111
24 2BRY FAD 0.027 0.40162 12
25 3ZBQ GDP 0.000005838 0.50332 14.4615
26 4EI7 GDP 0.00000003238 0.55247 35.6923
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