Receptor
PDB id Resolution Class Description Source Keywords
4PNO 0.97 Å NON-ENZYME: OTHER ESCHERICHIA COLI HFQ-RNA COMPLEX AT 0.97 A RESOLUTION ESCHERICHIA COLI RNA CHAPERONE HFQ RNA LSM RNA BINDING PROTEIN
Ref.: STRUCTURE OF AN ESCHERICHIA COLI HFQ:RNA COMPLEX AT ANGSTROM RESOLUTION. ACTA CRYSTALLOGR.,SECT.F V. 70 1492 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
U5P A:101;
Valid;
none;
submit data
324.181 C9 H13 N2 O9 P C1=CN...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4PNO 0.97 Å NON-ENZYME: OTHER ESCHERICHIA COLI HFQ-RNA COMPLEX AT 0.97 A RESOLUTION ESCHERICHIA COLI RNA CHAPERONE HFQ RNA LSM RNA BINDING PROTEIN
Ref.: STRUCTURE OF AN ESCHERICHIA COLI HFQ:RNA COMPLEX AT ANGSTROM RESOLUTION. ACTA CRYSTALLOGR.,SECT.F V. 70 1492 2014
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 4PNO - U5P C9 H13 N2 O9 P C1=CN(C(=O....
2 3RES - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 4PNO - U5P C9 H13 N2 O9 P C1=CN(C(=O....
2 3RES - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 4MML - U C9 H13 N2 O9 P O=C1N(C2OC....
4 4J6W - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
5 4J6X - UTP C9 H15 N2 O15 P3 C1=CN(C(=O....
6 4J5Y - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 4PNO - U5P C9 H13 N2 O9 P C1=CN(C(=O....
2 3RES - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 4MML - U C9 H13 N2 O9 P O=C1N(C2OC....
4 4J6W - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
5 4J6X - UTP C9 H15 N2 O15 P3 C1=CN(C(=O....
6 4J5Y - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: U5P; Similar ligands found: 120
No: Ligand ECFP6 Tc MDL keys Tc
1 U5P 1 1
2 44P 0.790323 0.941176
3 UDP 0.78125 0.984615
4 UTP 0.746269 0.984615
5 2KH 0.735294 0.955224
6 UDP UDP 0.727273 0.953846
7 UPU 0.694444 0.954545
8 UNP 0.690141 0.955224
9 URM 0.662338 0.913043
10 660 0.662338 0.913043
11 URI 0.661017 0.848485
12 U 0.661017 0.848485
13 UFM 0.641026 0.926471
14 GDU 0.641026 0.926471
15 UPG 0.641026 0.926471
16 GUD 0.641026 0.926471
17 U2F 0.6375 0.875
18 UPF 0.6375 0.875
19 Y6W 0.632911 0.875
20 UDH 0.628205 0.851351
21 UPP 0.628205 0.926471
22 UFG 0.617284 0.875
23 CJB 0.603175 0.80597
24 UDX 0.597561 0.926471
25 UAD 0.597561 0.926471
26 UDP GAL 0.597561 0.898551
27 3UC 0.588235 0.875
28 U U 0.585366 0.969697
29 UGB 0.583333 0.940298
30 USQ 0.583333 0.807692
31 UGA 0.583333 0.940298
32 5FU 0.57971 0.927536
33 G3N 0.576471 0.9
34 U3P 0.573529 0.953846
35 UA3 0.573529 0.953846
36 C 0.571429 0.941176
37 CH 0.571429 0.926471
38 CAR 0.571429 0.941176
39 C5P 0.571429 0.941176
40 UDM 0.568182 0.9
41 5BU 0.56338 0.927536
42 U4S 0.557143 0.763889
43 UD1 0.555556 0.913043
44 UD2 0.555556 0.913043
45 CSQ 0.550562 0.863014
46 CSV 0.550562 0.863014
47 U3S 0.541667 0.763889
48 U2S 0.541667 0.777778
49 CNU 0.540541 0.941176
50 S5P 0.535211 0.901408
51 16B 0.534247 0.901408
52 U2P 0.528571 0.939394
53 DU 0.527778 0.911765
54 UMP 0.527778 0.911765
55 HP7 0.526882 0.926471
56 UD7 0.526882 0.913043
57 MJZ 0.521277 0.9
58 UP6 0.521127 0.884058
59 UD4 0.515789 0.9
60 HWU 0.515789 0.887324
61 12V 0.515789 0.887324
62 BMP 0.513889 0.955224
63 UP5 0.510204 0.84
64 DKX 0.507246 0.732394
65 U6M 0.506849 0.969697
66 NUP 0.506849 0.927536
67 IUG 0.505155 0.797468
68 EPZ 0.5 0.9
69 U1S 0.5 0.76
70 JW5 0.5 0.955224
71 4TC 0.5 0.818182
72 EPU 0.49505 0.887324
73 A U 0.49505 0.815789
74 EEB 0.49505 0.887324
75 UDZ 0.494949 0.84
76 H2U 0.486111 0.911765
77 6AU 0.480519 0.969697
78 OMP 0.480519 0.969697
79 6CN 0.480519 0.941176
80 TKW 0.48 0.927536
81 UMF 0.479452 0.869565
82 UUA 0.477612 0.757576
83 U U U U 0.476744 0.954545
84 BMQ 0.472222 0.939394
85 PUP 0.47191 0.926471
86 5HM 0.467532 0.888889
87 O7E 0.463415 0.941176
88 ICR 0.460526 0.830986
89 UMA 0.458716 0.9
90 O7M 0.45679 0.941176
91 UC5 0.455696 0.885714
92 UTP U U U 0.454545 0.909091
93 CDP 0.45 0.927536
94 2TU 0.449275 0.760563
95 FNU 0.441558 0.876712
96 2QR 0.439655 0.810127
97 N3E 0.4375 0.743243
98 DUD 0.4375 0.898551
99 2OM 0.435897 0.925373
100 U22 0.434783 0.777778
101 U21 0.434783 0.797468
102 U20 0.434783 0.797468
103 DUT 0.433735 0.898551
104 CTP 0.433735 0.927536
105 8OP 0.428571 0.849315
106 8GM 0.421687 0.853333
107 5GW 0.420455 0.927536
108 U A A U 0.418803 0.853333
109 4RA 0.414634 0.842105
110 DUP 0.411765 0.873239
111 DUN 0.409639 0.873239
112 CDP MG 0.409639 0.861111
113 UD0 0.408 0.831169
114 UVC 0.407895 0.842857
115 UM3 0.407895 0.897059
116 C5G 0.404255 0.875
117 UPA 0.401869 0.828947
118 A U C C 0.401639 0.794872
119 A G U 0.4 0.7875
120 UAG 0.4 0.851351
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4PNO; Ligand: U5P; Similar sites found: 215
This union binding pocket(no: 1) in the query (biounit: 4pno.bio1) has 6 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4TMK T5A 0.000002689 0.60719 None
2 3K9W ADE 0.000002139 0.6039 None
3 3K9W 4PS 0.000002139 0.6039 None
4 4DA6 GA2 0.000000733 0.59462 None
5 1SAY PYR 0.000007276 0.59093 None
6 3QVL 5HY 0.0000007471 0.59068 None
7 1ZFJ IMP 0.000008583 0.5776 None
8 1W55 C 0.000001309 0.57681 None
9 3Q2I HP7 0.000003331 0.57331 None
10 1WKL ATP 0.000002073 0.57225 None
11 4HPP GLU 0.0000007803 0.568 None
12 1VQ2 DDN 0.000006934 0.55976 None
13 1OD6 PNS 0.000005556 0.55444 None
14 1G6O ADP 0.00001069 0.54584 None
15 1IZC PYR 0.000000729 0.54361 None
16 1QCA FUA 0.00002914 0.53588 None
17 1RSD PSB 0.0003988 0.52498 None
18 1G41 ADP 0.00004465 0.51981 None
19 1W55 GPP 0.000001798 0.51153 None
20 4NVP 7CH 0.00002103 0.51137 None
21 2CCV A2G 0.00001178 0.5052 None
22 2PAR TMP 0.00006353 0.50218 None
23 2JEN GLC GLC XYS XYS 0.00007219 0.50167 None
24 1WKL ADP 0.00009331 0.4936 None
25 2W24 LYS 0.00003562 0.49259 None
26 1BDB NAD 0.0004317 0.48936 None
27 1E4I NFG 0.00005298 0.48234 None
28 4FR3 0V4 0.0008747 0.47542 None
29 4FR3 LYS ARG ARG LYS SEP VAL 0.0008747 0.47542 None
30 2HMT NAI 0.0005205 0.46961 None
31 1G7V PAI 0.0003554 0.46778 None
32 3CL7 HYN 0.0001093 0.46661 None
33 1NME 159 0.00003576 0.4653 None
34 3NOJ PYR 0.0001346 0.46508 None
35 2C1Q BTN 0.0004251 0.46465 None
36 1EDO NAP 0.001545 0.46409 None
37 3OIG NAD 0.001192 0.46319 None
38 3OIG IMJ 0.0003189 0.4619 None
39 1ZK4 NAP 0.002504 0.45994 None
40 1ZK4 AC0 0.002504 0.45994 None
41 2JEN GLC GLC BGC XYS BGC XYS 0.002479 0.45714 None
42 1SS4 CIT 0.008505 0.45288 None
43 1JA9 NDP 0.002899 0.45231 None
44 3CH5 GDP 0.0005906 0.45139 None
45 1GXU 2HP 0.000001403 0.45137 None
46 1I9G SAM 0.001335 0.45085 None
47 3PHQ KDO 0.009517 0.45 None
48 4LTN FMN 0.001363 0.44852 None
49 4LTN NAI 0.001689 0.44852 None
50 2H6B 3C4 0.002261 0.44835 None
51 1UQX MMA 0.0003519 0.44745 None
52 2GJ3 FAD 0.0007003 0.44498 None
53 4EKV BTN 0.00088 0.44459 None
54 1LDM NAD 0.00392 0.44406 None
55 2BLE 5GP 0.003448 0.44365 None
56 3BY8 MLT 0.001987 0.4432 None
57 1NPL MAN 0.000422 0.4407 None
58 1LO8 4CA 0.004773 0.43905 None
59 1WL4 COA 0.002383 0.43863 None
60 2QXX TTP 0.001516 0.43783 None
61 3V91 UPG 0.003581 0.43505 None
62 4LBP 1WG 0.001136 0.43465 None
63 3A8U PLP 0.0008178 0.43364 None
64 1DRV A3D 0.004132 0.43248 None
65 2GN2 C5P 0.0004278 0.4319 None
66 3Q3C NAD 0.006345 0.428 None
67 1Q3Q ANP 0.007582 0.42773 None
68 3UXL CFI 0.02059 0.42358 None
69 2FMD MAN MAN 0.00107 0.42175 None
70 1D09 PAL 0.03328 0.41992 None
71 4BPM GSH 0.00217 0.41927 None
72 1OTH PAO 0.003921 0.41785 None
73 1JA9 PYQ 0.003237 0.4171 None
74 2P4T NAP 0.00382 0.41701 None
75 4KCF AKM 0.01108 0.41634 None
76 2JE7 XMM 0.003093 0.41496 None
77 3F81 STT 0.01678 0.41395 None
78 3ZZS TRP 0.006109 0.41382 None
79 3ZZL TRP 0.007845 0.4137 None
80 4BPM LVJ 0.004625 0.40901 None
81 4KCF FMN 0.009144 0.409 None
82 3EM1 TYD 0.003946 0.40703 None
83 1MG1 MAL 0.003834 0.40498 None
84 1H6W SER LEU ASN TYR ILE ILE LYS VAL LYS GLU 0.02125 0.40414 None
85 2ZI8 SDT 0.00746 0.4031 None
86 1NMU MTT 0.04307 0.4021 None
87 1NXJ TLA 0.002667 0.40203 None
88 1H9A NAP 0.03899 0.40114 None
89 3TO7 COA 0.01567 0.40059 None
90 2QS8 MET 0.008739 0.40044 None
91 4IAE 1DX 0.02659 0.40006 None
92 3RO7 TDR 0.00004074 0.54675 0.754717
93 3C2O NTM 0.000006954 0.57902 2.77778
94 1JH7 UVC 0.00003274 0.50804 2.77778
95 3FSJ D7K 0.001888 0.46034 2.77778
96 1RRC ADP 0.0001518 0.45725 2.77778
97 1CR1 TTP 0.00001038 0.55768 4.16667
98 2OWZ CIT 0.0001213 0.46087 4.16667
99 1EXB NDP 0.002479 0.45652 4.16667
100 2A0W DIH 0.006189 0.41188 4.16667
101 2HVK TBA 0.00005299 0.40641 4.16667
102 5D6C 57S 0.02946 0.40517 4.16667
103 1RM4 NDP 0.03126 0.40286 4.16667
104 4HZD COA 0.01317 0.40055 4.16667
105 2Q6K ADN 0.000001126 0.602 5.55556
106 3EJ0 11X 0.00005741 0.47912 5.55556
107 3K37 BCZ 0.0009854 0.47643 5.55556
108 3MB5 SAM 0.0004622 0.47366 5.55556
109 4QN7 G39 0.0002404 0.46949 5.55556
110 3CXO 3LR 0.00127 0.43277 5.55556
111 3CXO 1N5 0.00313 0.42039 5.55556
112 1XMV ADP 0.000001977 0.5731 6.94444
113 1XP8 AGS 0.00001286 0.53229 6.94444
114 4M6T SAM 0.0000516 0.50014 6.94444
115 1F8F NAD 0.005687 0.43153 6.94444
116 1ME8 RVP 0.01739 0.42298 6.94444
117 1FA2 DOM 0.003549 0.41556 6.94444
118 1KW6 BPY 0.00001393 0.54688 8.33333
119 2FWP ICR 0.00001431 0.51799 8.33333
120 1GSA ADP 0.0005448 0.46879 8.33333
121 4N02 FNR 0.002917 0.44211 8.33333
122 1HV9 COA 0.00233 0.44139 8.33333
123 2FWP CIT 0.001742 0.4303 8.33333
124 2BMK PDD 0.004156 0.42539 8.33333
125 2NZ2 CIR 0.002059 0.42171 8.33333
126 1GSA GSH 0.005882 0.42073 8.33333
127 5T63 ALA ALA ALA ALA 0.00002941 0.41914 8.33333
128 1LTH NAD 0.01046 0.41892 8.33333
129 3VOZ 04A 0.001062 0.4176 8.33333
130 2NZ2 ASP 0.0002845 0.41053 8.33333
131 4KQL 1SG 0.02216 0.41053 8.33333
132 1HV9 UD1 0.01346 0.40876 8.33333
133 1O6B ADP 0.000003509 0.55534 9.72222
134 4IVG ANP 0.0001804 0.49061 9.72222
135 2YYJ FAD 0.001058 0.4775 9.72222
136 2YYJ 4HP 0.001058 0.4775 9.72222
137 2IMP NAI 0.006416 0.44203 9.72222
138 2IMP LAC 0.000303 0.44189 9.72222
139 4HE2 AMP 0.00204 0.42763 9.72222
140 4QN6 LNV 0.006015 0.41628 9.72222
141 1ML4 PAL 0.004735 0.40405 9.72222
142 3D2M COA 0.000007644 0.58114 11.1111
143 1GR0 NAD 0.0008043 0.47899 11.1111
144 2NLI LAC 0.0009423 0.46752 11.1111
145 2NLI FMN 0.0008642 0.46752 11.1111
146 1VCO GLN 0.0003292 0.45208 11.1111
147 4AF0 IMP 0.001997 0.44552 11.1111
148 4AF0 MOA 0.0007779 0.43446 11.1111
149 1P4C FMN 0.009557 0.42872 11.1111
150 1MVN PCO 0.01201 0.41893 11.1111
151 4OYA 1VE 0.03341 0.41751 11.1111
152 3M0J OAF 0.009295 0.40194 11.1111
153 2QIA U20 0.02851 0.40094 11.1111
154 4A8T PAO 0.00000002567 0.66316 12.5
155 1JQ5 NAD 0.00005614 0.5537 12.5
156 3MMR ABH 0.00001824 0.53611 12.5
157 1DXY NAD 0.00007405 0.53335 12.5
158 4C25 13P 0.0001072 0.47415 12.5
159 4GQB 0XU 0.0006476 0.46939 12.5
160 4AP9 1PS 0.00009867 0.4598 12.5
161 3O03 NAP 0.001686 0.45529 12.5
162 1DXY COI 0.0002584 0.45433 12.5
163 4MWV BCZ 0.001113 0.44556 12.5
164 3O03 GCO 0.0008298 0.41669 12.5
165 4MOB COA 0.009045 0.41021 12.5
166 1RY2 AMP 0.005516 0.40388 12.5
167 3IU9 T07 0.03174 0.40195 12.5
168 1OFH ADP 0.000001155 0.58969 13.8889
169 2RHW C0E 0.001781 0.45728 13.8889
170 2BGM NAJ 0.002921 0.44522 13.8889
171 4AAW R84 0.01095 0.41496 13.8889
172 4HZX G39 0.007895 0.41359 13.8889
173 2GGH NLQ 0.01147 0.40295 13.8889
174 1SAZ ACP 0.000003344 0.58403 15.2778
175 2ET1 GLV 0.000008444 0.53161 15.2778
176 4KS1 2H8 0.001416 0.44785 15.2778
177 4CMF PXG 0.005199 0.43002 15.2778
178 1WVC CTP 0.0001773 0.51283 16.6667
179 4TSK NDP 0.001575 0.45653 16.6667
180 1V5F TPP 0.02711 0.43339 16.6667
181 1V5F FAD 0.02711 0.43339 16.6667
182 2BNE U5P 0.004412 0.41768 16.6667
183 4TSK TLA 0.003366 0.40345 16.6667
184 2X61 NGA GAL SIA 0.0003178 0.48582 18.0556
185 2X61 CH 0.0001537 0.4824 18.0556
186 2Q1A 2KT 0.0002245 0.45092 18.0556
187 3HU3 AGS 0.0104 0.42462 18.0556
188 2AEB ABH 0.003823 0.40993 18.0556
189 2PJL 047 0.009166 0.40514 18.0556
190 4G1V FAD 0.00004262 0.54587 19.4444
191 1A5Z OXM 0.0002176 0.49607 19.4444
192 1K97 ASP 0.01081 0.43312 19.4444
193 1K97 CIR 0.01081 0.43312 19.4444
194 4IRL MTT 0.04295 0.40534 19.4444
195 1Z34 2FD 0.00005265 0.51382 20.8333
196 1H82 GZZ 0.01234 0.42423 22.2222
197 1OMZ UD2 0.00004314 0.50962 23.6111
198 1YBH P22 0.0001055 0.47769 23.6111
199 3L8W XAN 0.0005197 0.47682 23.6111
200 1YBH FAD 0.002386 0.46419 23.6111
201 4QDC ASD 0.001675 0.42591 23.6111
202 2PN6 GLN 0.0000005907 0.6132 26.3889
203 2P2V CSF 0.000535 0.47102 26.3889
204 2P8B NSK 0.000003904 0.59803 27.7778
205 4A3R CIT 0.004534 0.41896 29.1667
206 4HGP KDO 0.004571 0.41882 30.5556
207 2VJJ RAM GLC GAL NAG NAG GLC 0.02007 0.40518 30.5556
208 1X1T NAD 0.001358 0.46783 34.7222
209 2R7K ACP 0.00001814 0.56244 36.1111
210 2R7K AMZ 0.00001814 0.56244 36.1111
211 1T26 GBD 0.001003 0.48409 36.1111
212 1T26 NAI 0.001003 0.48409 36.1111
213 1NVV GNP 0.0008446 0.46629 36.1111
214 1NVU GTP 0.002434 0.44701 36.1111
215 1YOE RIB 0.00145 0.43055 38.8889
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