Receptor
PDB id Resolution Class Description Source Keywords
5EY0 1.6 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF CODY FROM STAPHYLOCOCCUS AUREUS WITH GT STAPHYLOCOCCUS AUREUS (STRAIN MU3 / AT700698) GTP-SENSING PLEIOTROPIC TRANSCRIPTION REGULATOR TRANSCRIPT
Ref.: THE STRUCTURE OF THE PLEIOTROPIC TRANSCRIPTION REGU CODY PROVIDES INSIGHT INTO ITS GTP-SENSING MECHANIS NUCLEIC ACIDS RES. V. 44 9483 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GTP A:302;
B:302;
Valid;
Valid;
none;
none;
Kd = 2.26 mM
523.18 C10 H16 N5 O14 P3 c1nc2...
ILE A:301;
B:301;
Valid;
Valid;
none;
none;
submit data
131.173 C6 H13 N O2 CC[C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5EY0 1.6 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF CODY FROM STAPHYLOCOCCUS AUREUS WITH GT STAPHYLOCOCCUS AUREUS (STRAIN MU3 / AT700698) GTP-SENSING PLEIOTROPIC TRANSCRIPTION REGULATOR TRANSCRIPT
Ref.: THE STRUCTURE OF THE PLEIOTROPIC TRANSCRIPTION REGU CODY PROVIDES INSIGHT INTO ITS GTP-SENSING MECHANIS NUCLEIC ACIDS RES. V. 44 9483 2016
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 257 families.
1 5EY1 Kd = 2.26 mM GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
2 5EY0 Kd = 2.26 mM GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 222 families.
1 5EY1 Kd = 2.26 mM GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
2 5EY0 Kd = 2.26 mM GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 185 families.
1 5EY1 Kd = 2.26 mM GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
2 5EY0 Kd = 2.26 mM GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GTP; Similar ligands found: 147
No: Ligand ECFP6 Tc MDL keys Tc
1 GTP 1 1
2 GP3 0.921053 0.973684
3 GDP 0.909091 1
4 GSP 0.853659 0.948718
5 GNH 0.82716 0.986667
6 G1R 0.819277 0.986667
7 GAV 0.811765 0.961039
8 GNP 0.809524 0.973684
9 GCP 0.797619 0.973684
10 5GP 0.797468 0.986486
11 G 0.797468 0.986486
12 GMV 0.764706 0.973684
13 G2R 0.764045 0.961039
14 G5P 0.755319 0.973684
15 GTG 0.752688 0.936709
16 G2P 0.747126 0.961039
17 G3A 0.744681 0.973684
18 GDD 0.741935 0.961039
19 GKE 0.741935 0.961039
20 GDC 0.741935 0.961039
21 0O2 0.736264 0.986486
22 GP2 0.729412 0.961039
23 6CK 0.726316 0.936709
24 Y9Z 0.723404 0.902439
25 GPG 0.717391 0.961039
26 GFB 0.715789 0.961039
27 GDR 0.715789 0.961039
28 GDP MG 0.712644 0.923077
29 GDP BEF 0.704545 0.9
30 GPD 0.704082 0.925
31 JB2 0.693878 0.961039
32 GKD 0.693878 0.961039
33 GCP G 0.692308 0.935065
34 GDX 0.686869 0.973684
35 ALF 5GP 0.685393 0.888889
36 GTP MG 0.681319 0.923077
37 BEF GDP 0.681319 0.888889
38 GH3 0.681319 0.973333
39 YGP 0.677083 0.901235
40 G3D 0.67033 0.986486
41 GDP AF3 0.659574 0.888889
42 GDP ALF 0.659574 0.888889
43 DGT 0.659341 0.923077
44 GMP 0.658228 0.88
45 G4P 0.655914 0.986486
46 JB3 0.653846 0.948718
47 NGD 0.647619 0.961039
48 CAG 0.642202 0.880952
49 2MD 0.62963 0.891566
50 G G 0.622449 0.935065
51 MGP 0.619565 0.961039
52 U2G 0.616822 0.936709
53 6G0 0.612903 0.961039
54 MGD 0.612613 0.891566
55 TPG 0.608696 0.840909
56 CG2 0.605505 0.936709
57 GDP 7MG 0.601942 0.911392
58 FEG 0.601852 0.879518
59 ZGP 0.59633 0.869048
60 MD1 0.591304 0.891566
61 PGD 0.591304 0.925
62 3GP 0.590909 0.946667
63 GPX 0.581633 0.946667
64 DGI 0.580645 0.923077
65 IDP 0.576087 0.972973
66 DBG 0.567797 0.948718
67 FE9 0.555556 0.776596
68 2GP 0.555556 0.96
69 G4M 0.547619 0.880952
70 BGO 0.544643 0.924051
71 I2C FE2 CMO CMO 0.538462 0.808989
72 ATP 0.537634 0.92
73 G1G 0.533898 0.925
74 AQP 0.531915 0.92
75 5FA 0.531915 0.92
76 G A A A 0.525862 0.923077
77 U A G G 0.521368 0.935065
78 01G 0.518868 0.902439
79 ITT 0.510638 0.868421
80 P2G 0.510638 0.883117
81 GGM 0.504274 0.901235
82 G1R G1R 0.504065 0.924051
83 DGP 0.5 0.910256
84 PGD O 0.5 0.850575
85 MGO 0.5 0.864198
86 P1G 0.5 0.871795
87 DG 0.5 0.910256
88 GTA 0.495495 0.936709
89 B4P 0.489362 0.894737
90 AP5 0.489362 0.894737
91 IMP 0.489362 0.959459
92 7DT 0.484536 0.906667
93 G G U 0.482143 0.935065
94 GPC 0.479339 0.879518
95 G C 0.478992 0.9
96 BA3 0.478723 0.894737
97 ADP 0.473684 0.92
98 G2Q 0.471698 0.961039
99 G7M 0.46875 0.948052
100 25L 0.458716 0.907895
101 A2D 0.457447 0.894737
102 RGT 0.45045 0.909091
103 AGS 0.45 0.873418
104 SAP 0.45 0.873418
105 SGP 0.44898 0.82716
106 U G A 0.448529 0.888889
107 A4P 0.445378 0.869048
108 G G G RPC 0.442623 0.875
109 ACQ 0.441176 0.896104
110 ANP 0.441176 0.896104
111 8GT 0.441176 0.875
112 APC G U 0.44 0.886076
113 G U34 0.438017 0.888889
114 6AD 0.436893 0.841463
115 G G G C 0.433071 0.9125
116 UP5 0.432203 0.873418
117 35G 0.431373 0.933333
118 C2E 0.431373 0.921053
119 PCG 0.431373 0.933333
120 A G C C 0.429688 0.911392
121 5GP 5GP 0.427184 0.883117
122 TAT 0.427184 0.884615
123 APR 0.425743 0.894737
124 AR6 0.425743 0.894737
125 AN2 0.424242 0.907895
126 7DD 0.424242 0.906667
127 DG DG 0.423423 0.865854
128 AD9 0.421569 0.896104
129 M33 0.42 0.883117
130 7D4 0.42 0.835443
131 UCG 0.419847 0.911392
132 H6Y 0.419048 0.946667
133 G C C C 0.416667 0.924051
134 ACP 0.415842 0.896104
135 T5A 0.414634 0.802326
136 MGQ 0.412844 0.935897
137 ADQ 0.412844 0.871795
138 A1R 0.412844 0.839506
139 MGT 0.411215 0.823529
140 A G U 0.410072 0.888889
141 93A 0.41 0.833333
142 A22 0.407407 0.907895
143 CA0 0.405941 0.896104
144 ATF 0.40566 0.884615
145 AGO 0.404762 0.888889
146 MGV 0.401786 0.890244
147 CGP 0.4 0.86747
Ligand no: 2; Ligand: ILE; Similar ligands found: 11
No: Ligand ECFP6 Tc MDL keys Tc
1 ILE 1 1
2 VAL 0.565217 0.727273
3 MD0 0.551724 0.655172
4 THR 0.541667 0.6
5 VAH 0.538462 0.703704
6 DAL 0.5 0.714286
7 ABA 0.5 0.782609
8 ALA 0.5 0.714286
9 DBB 0.5 0.782609
10 LEU 0.428571 0.791667
11 NVA 0.428571 0.833333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5EY0; Ligand: ILE; Similar sites found: 8
This union binding pocket(no: 1) in the query (biounit: 5ey0.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1TD2 PXL 0.006688 0.40529 2.55474
2 1QZR ANP 0.03814 0.40128 2.91971
3 5H2D ERG 0.01479 0.41887 3.64964
4 1VR0 3SL 0.03107 0.41024 4.74453
5 2TCL RO4 0.01866 0.40997 5.32544
6 5SYM 71Q 0.01594 0.41123 5.65217
7 4C0R GDS 0.006687 0.43863 6.45161
8 4CZG QH3 0.02402 0.42305 6.93431
Pocket No.: 2; Query (leader) PDB : 5EY0; Ligand: GTP; Similar sites found: 92
This union binding pocket(no: 2) in the query (biounit: 5ey0.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2GBB CIT 0.003462 0.42769 None
2 1LR8 IHS 0.0009787 0.40789 None
3 4X8D AVI 0.005654 0.43652 2.18978
4 5L7G 6QE 0.01042 0.41623 2.18978
5 5UIU 8CG 0.0282 0.40303 2.18978
6 3QCP FAD 0.02664 0.40042 2.18978
7 1XZ3 ICF 0.00849 0.4305 2.29885
8 5KAU RHQ 0.009537 0.41287 2.42424
9 4BTK DTQ 0.006845 0.41788 2.55474
10 2Z48 NGA 0.00816 0.41687 2.55474
11 1GEG GLC 0.04689 0.40728 2.73438
12 4DXJ IPE 0.02869 0.40502 2.91971
13 4DXJ 0M9 0.03103 0.40092 2.91971
14 2VWA PTY 0.006966 0.42755 2.9703
15 3LE7 ADE 0.01739 0.40225 3.06513
16 3W6C NAG NAG 0.02272 0.40781 3.27869
17 3BU5 ATP 0.00849 0.41338 3.28467
18 2QLU ADE 0.01811 0.40686 3.28467
19 1AE1 NAP 0.02589 0.40953 3.2967
20 1GHE ACO 0.008031 0.42341 3.38983
21 4OMJ 2TX 0.01352 0.4229 3.64964
22 4LJ3 C2E 0.01785 0.40624 3.64964
23 3ITJ CIT 0.02783 0.41403 4.0146
24 1H6H PIB 0.00547 0.42144 4.1958
25 4LSJ LSJ 0.006687 0.42398 4.26357
26 4P6X HCY 0.004157 0.43222 4.31373
27 4RW3 PLM 0.03025 0.40327 4.37956
28 1BWO LPC 0.007501 0.41791 4.44444
29 4KVX ACO 0.0283 0.40044 4.48718
30 5HGZ ACO 0.002077 0.45405 4.52675
31 4HIA FMN 0.01555 0.42203 4.54545
32 1SR7 MOF 0.01458 0.42005 4.6332
33 5JNN 6LM 0.01364 0.41204 4.73684
34 3TDC 0EU 0.000005925 0.66741 4.74453
35 3KDU NKS 0.01507 0.43399 4.74453
36 3FUR Z12 0.01726 0.4292 4.74453
37 4BIX ADP 0.001915 0.41994 4.74453
38 1P0H ACO 0.04968 0.41538 4.74453
39 3G9E RO7 0.03398 0.40342 4.74453
40 1QPR PHT 0.01801 0.40039 4.74453
41 5FQK 6NT 0.009036 0.41527 4.83271
42 1Q2C COA 0.01768 0.40491 4.93827
43 1YKI FMN 0.01889 0.41431 5.06912
44 1YKI NFZ 0.02195 0.41431 5.06912
45 5CX6 CDP 0.01308 0.40855 5.10949
46 3BP1 GUN 0.02823 0.40161 5.10949
47 3KU0 ADE 0.01441 0.40596 5.17928
48 3IX9 MTX 0.003287 0.41497 5.26316
49 2B9H ADP 0.01205 0.40794 5.38244
50 3WCA FPS 0.01141 0.42296 5.47445
51 2JFZ DGL 0.0415 0.41731 5.4902
52 3VRV YSD 0.02608 0.42128 5.53506
53 4B7P 9UN 0.02518 0.42049 5.65217
54 3TL1 JRO 0.01459 0.40212 5.66038
55 5JO1 6LM 0.00357 0.43543 5.83942
56 4I4B 1CV 0.02718 0.4095 5.83942
57 4WH9 3M8 0.006909 0.43186 6.01093
58 2Q2Y ADP 0.01748 0.44615 6.20438
59 2Q2Y MKR 0.01748 0.44615 6.20438
60 5EXK 5AD 0.01458 0.40517 6.20438
61 4DV8 0LX 0.02417 0.41215 6.84411
62 2JHP GUN 0.01394 0.42452 6.93431
63 2EV1 OLA 0.01607 0.40695 7.20721
64 5CHR 4NC 0.01403 0.40642 7.29927
65 5V4R MGT 0.008153 0.4256 7.40741
66 2HHP FLC 0.0005811 0.48333 7.66423
67 3KO0 TFP 0.01455 0.40513 7.92079
68 4J7U YTZ 0.01468 0.43119 8.0292
69 4J7U NAP 0.01468 0.43119 8.0292
70 3JRS A8S 0.008416 0.41153 8.65385
71 1VPV PLM 0.01532 0.41385 8.75912
72 3SVJ 4LI 0.01808 0.40282 8.86699
73 4ORM 2V6 0.02218 0.43473 9.48905
74 4ORM FMN 0.02218 0.43473 9.48905
75 4ORM ORO 0.02218 0.43473 9.48905
76 4MRP GSH 0.03437 0.40164 9.85401
77 5UGW GSH 0.001057 0.44796 10.2857
78 2QES ADE 0.0158 0.40347 11.1111
79 3FW3 GLC 0.01795 0.40179 11.3139
80 4WZ8 3W7 0.04929 0.40245 11.6788
81 4FHD 0TT 0.01079 0.4267 12.4088
82 4FHD EEM 0.01079 0.4267 12.4088
83 3AIH BMA MAN MAN 0.001697 0.45409 12.9032
84 4ZGM 32M 0.00472 0.44103 13.1148
85 4IEH 1E9 0.01756 0.4066 15.3846
86 2XMY CDK 0.02546 0.43083 16.7883
87 2DYR TGL 0.01521 0.42028 19.2661
88 3RV5 DXC 0.006445 0.44158 20.2247
89 3G08 FEE 0.01631 0.436 22.2222
90 5L2J 70E 0.0345 0.42533 22.449
91 5L2J 6UL 0.03287 0.42533 22.449
92 5U98 1KX 0.03473 0.42093 23.2323
Pocket No.: 3; Query (leader) PDB : 5EY0; Ligand: ILE; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5ey0.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5EY0; Ligand: GTP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5ey0.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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