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 AND GTP-GAMMA-S BACILLUS SUBTILIS CELL DIVISION PROTEIN TUBULIN HOMOLOG GTP-BINDING POLYMERGTPASE CELL CYCLE STRUCTURAL GENOMICS PSI-2 PROTEIN STRINITIATIVE ACCELERATED TECHNOLOGIES CENTER FOR GENE TO 3D STRUCTURE ATCG3D
Ref.: COMBINED PROTEIN CONSTRUCT AND SYNTHETIC GENE ENGIN FOR HETEROLOGOUS PROTEIN EXPRESSION AND CRYSTALLIZA 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 AND GTP-GAMMA-S BACILLUS SUBTILIS CELL DIVISION PROTEIN TUBULIN HOMOLOG GTP-BINDING POLYMERGTPASE CELL CYCLE STRUCTURAL GENOMICS PSI-2 PROTEIN STRINITIATIVE ACCELERATED TECHNOLOGIES CENTER FOR GENE TO 3D STRUCTURE ATCG3D
Ref.: COMBINED PROTEIN CONSTRUCT AND SYNTHETIC GENE ENGIN FOR HETEROLOGOUS PROTEIN EXPRESSION AND CRYSTALLIZA 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 29 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 (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 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 6RVQ - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
8 6SI9 Kd = 18.2 nM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 6RVP - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
10 5H5G - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
11 6RVN Kd = 18.2 nM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
12 6KVP - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
13 5H5H - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
14 5H5I - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
15 6KVQ Kd = 0.88 uM DVX C33 H25 B Br F7 N4 O5 [B-]1(n2c(....
16 5XDW - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
17 5MN4 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
18 5XDU - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
19 6LL5 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
20 6LL6 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
21 6UMK - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
22 6UNX - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
50% Homology Family (31)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 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 6RVQ - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
8 6SI9 Kd = 18.2 nM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 6RVP - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
10 5H5G - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
11 6RVN Kd = 18.2 nM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
12 6KVP - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
13 5H5H - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
14 5H5I - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
15 6KVQ Kd = 0.88 uM DVX C33 H25 B Br F7 N4 O5 [B-]1(n2c(....
16 5XDW - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
17 5MN4 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
18 5XDU - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
19 1W5F - G2P C11 H18 N5 O13 P3 c1nc2c(n1[....
20 1RQ2 ic50 = 3 mM CIT C6 H8 O7 C(C(=O)O)C....
21 1RLU - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
22 1W5B - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
23 1W5A - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
24 1W58 - G2P C11 H18 N5 O13 P3 c1nc2c(n1[....
25 2VAP - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
26 6LL5 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
27 6LL6 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
28 6UMK - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
29 6UNX - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
30 2R6R - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
31 2R75 Kd = 714 nM 01G C14 H23 N6 O15 P3 C1COCCN1c2....
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
Ligand no: 2; Ligand: GSP; Similar ligands found: 135
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 9GM 0.770115 0.925
9 GNP 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 GPD 0.69 0.880952
31 GDX 0.69 0.925
32 GDP BEF 0.681319 0.888889
33 GTP MG 0.673913 0.911392
34 ALF 5GP 0.67033 0.847059
35 0O2 0.666667 0.935897
36 YGP 0.663265 0.858824
37 JB3 0.657143 0.902439
38 GDP AF3 0.645833 0.847059
39 GDP ALF 0.645833 0.847059
40 GMP 0.641975 0.835443
41 G3D 0.638298 0.935897
42 NGD 0.635514 0.91358
43 2MD 0.633027 0.894118
44 CAG 0.630631 0.840909
45 G4P 0.625 0.935897
46 FEG 0.62037 0.83908
47 U2G 0.62037 0.891566
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 KB7 0.595745 0.788235
53 3GP 0.595506 0.898734
54 GDP 7MG 0.590476 0.86747
55 GH3 0.581633 0.924051
56 PGD 0.581197 0.926829
57 MD1 0.581197 0.894118
58 2GP 0.577778 0.911392
59 DGT 0.561224 0.878049
60 DBG 0.558333 0.902439
61 KBD 0.553398 0.788235
62 G1G 0.550847 0.880952
63 AGS 0.547368 0.924051
64 QBQ 0.546392 0.935897
65 FE9 0.546219 0.8
66 G4M 0.539062 0.840909
67 KBJ 0.53271 0.761364
68 MGP 0.525253 0.91358
69 GPX 0.524272 0.898734
70 BGO 0.521739 0.879518
71 I2C FE2 CMO CMO 0.520661 0.774194
72 DGI 0.520408 0.878049
73 6G0 0.52 0.91358
74 IDP 0.515464 0.923077
75 R5I 0.51 0.898734
76 R7I 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 CZF 0.49 0.886076
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 DGP 0.474227 0.865854
88 DG 0.474227 0.865854
89 BA3 0.46875 0.85
90 AP5 0.463918 0.85
91 B4P 0.463918 0.85
92 IMP 0.463918 0.910256
93 G2Q 0.462963 0.91358
94 APC G U 0.456693 0.843373
95 ATP 0.45 0.873418
96 HEJ 0.45 0.873418
97 A2D 0.447917 0.85
98 5FA 0.445545 0.873418
99 AQP 0.445545 0.873418
100 G7M 0.444444 0.901235
101 01G 0.442478 0.860465
102 SGP 0.44 0.876543
103 ITT 0.44 0.825
104 JSQ 0.436893 0.831325
105 HFD 0.436893 0.831325
106 GZ0 0.433333 0.902439
107 AT4 0.43 0.911392
108 AN2 0.43 0.8625
109 A4P 0.42623 0.829545
110 UCG 0.424242 0.86747
111 C2E 0.423077 0.875
112 PCG 0.423077 0.886076
113 35G 0.423077 0.886076
114 MGO 0.420561 0.823529
115 ADP 0.42 0.873418
116 ANP 0.419048 0.851852
117 5GP 5GP 0.419048 0.839506
118 M7G A2M G 0.418301 0.774194
119 ADQ 0.418182 0.829268
120 APR 0.417476 0.85
121 7DT 0.417476 0.860759
122 AR6 0.417476 0.85
123 PRT 0.417391 0.910256
124 HQG 0.416667 0.8625
125 C1Z 0.415929 0.935897
126 AD9 0.413462 0.851852
127 UP5 0.413223 0.831325
128 A22 0.412844 0.8625
129 25L 0.412281 0.8625
130 M33 0.411765 0.839506
131 JBT 0.410405 0.783505
132 ACP 0.407767 0.851852
133 6YZ 0.407407 0.851852
134 ACQ 0.40566 0.851852
135 A1R 0.405405 0.8
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
Ligand no: 2; Ligand: GSP; Similar ligands found: 18
No: Ligand Similarity coefficient
1 BEF GDP 0.9951
2 ALF GDP 0.9840
3 BEF ADP 0.9761
4 DTP 0.9655
5 ADP ALF 0.9598
6 GDP MG 0.9446
7 ADP AF3 0.9389
8 UTP 0.9143
9 CTP 0.9100
10 ATF 0.9078
11 ADP MG 0.8998
12 DSZ 0.8805
13 APC 0.8789
14 AMO 0.8780
15 DAT 0.8737
16 ADP BEF 0.8685
17 AV2 0.8567
18 SAM 0.8566
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2RHO; 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: 1) in the query (biounit: 2rho.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2RHO; 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: 2rho.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
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