Receptor
PDB id Resolution Class Description Source Keywords
2VPR 2.49 Å NON-ENZYME: TRANSCRIPT_TRANSLATE TET REPRESSOR CLASS H IN COMPLEX WITH 5A,6- ANHYDROTETRACYCLINE-MG PASTEURELLA MULTOCIDA TRANSCRIPTION METAL-BINDING ANTIBIOTIC RESISTANCE TRANSCRREGULATOR TRANSCRIPTION REGULATION DNA-BINDING
Ref.: TET REPRESSOR INDUCTION BY TETRACYCLINE: A MOLECULA DYNAMICS, CONTINUUM ELECTROSTATICS, AND CRYSTALLOGR STUDY J.MOL.BIOL. V. 378 896 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:1207;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
SO4 A:1208;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
TDC A:1206;
Valid;
none;
submit data
426.419 C22 H22 N2 O7 Cc1c2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2VPR 2.49 Å NON-ENZYME: TRANSCRIPT_TRANSLATE TET REPRESSOR CLASS H IN COMPLEX WITH 5A,6- ANHYDROTETRACYCLINE-MG PASTEURELLA MULTOCIDA TRANSCRIPTION METAL-BINDING ANTIBIOTIC RESISTANCE TRANSCRREGULATOR TRANSCRIPTION REGULATION DNA-BINDING
Ref.: TET REPRESSOR INDUCTION BY TETRACYCLINE: A MOLECULA DYNAMICS, CONTINUUM ELECTROSTATICS, AND CRYSTALLOGR STUDY J.MOL.BIOL. V. 378 896 2008
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 257 families.
1 2VPR - TDC C22 H22 N2 O7 Cc1c2cccc(....
70% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 222 families.
1 2VPR - TDC C22 H22 N2 O7 Cc1c2cccc(....
2 1ORK Kd = 1.56 nM ATC C25 H30 N4 O8 CN(C)CC(=O....
3 5FKK - TDC C22 H22 N2 O7 Cc1c2cccc(....
4 2TCT Ka ~ 10000000 M^-1 CTC C22 H23 Cl N2 O8 C[C@]1(c2c....
5 5FKN - TDC C22 H22 N2 O7 Cc1c2cccc(....
6 2VKV Ka = 45000000 M^-1 TDC C22 H22 N2 O7 Cc1c2cccc(....
7 2X9D - ITC C22 H23 Cl N2 O8 C[C@@]1(c2....
8 4D7M Ka = 980000000000 M^-1 TDC C22 H22 N2 O7 Cc1c2cccc(....
9 5FKO - TDC C22 H22 N2 O7 Cc1c2cccc(....
10 2FJ1 - CTC C22 H23 Cl N2 O8 C[C@]1(c2c....
11 5FKL - TDC C22 H22 N2 O7 Cc1c2cccc(....
12 2XB5 - I7T C21 H21 I N2 O7 CN(C)[C@H]....
13 2TRT - TAC C22 H24 N2 O8 C[C@]1(c2c....
14 4D7N Ka = 23000000 M^-1 TDC C22 H22 N2 O7 Cc1c2cccc(....
15 5FKM - TDC C22 H22 N2 O7 Cc1c2cccc(....
16 2VKE - TAC C22 H24 N2 O8 C[C@]1(c2c....
17 2O7O - DXT C22 H24 N2 O8 C[C@H]1c2c....
18 3FK7 Kd = 0.75 nM 4DM C20 H17 N O7 Cc1c2cccc(....
19 2X6O - 2TC C22 H21 Cl N2 O7 C[C@@]1(c2....
50% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 185 families.
1 2VPR - TDC C22 H22 N2 O7 Cc1c2cccc(....
2 1ORK Kd = 1.56 nM ATC C25 H30 N4 O8 CN(C)CC(=O....
3 5FKK - TDC C22 H22 N2 O7 Cc1c2cccc(....
4 2TCT Ka ~ 10000000 M^-1 CTC C22 H23 Cl N2 O8 C[C@]1(c2c....
5 5FKN - TDC C22 H22 N2 O7 Cc1c2cccc(....
6 2VKV Ka = 45000000 M^-1 TDC C22 H22 N2 O7 Cc1c2cccc(....
7 2X9D - ITC C22 H23 Cl N2 O8 C[C@@]1(c2....
8 4D7M Ka = 980000000000 M^-1 TDC C22 H22 N2 O7 Cc1c2cccc(....
9 5FKO - TDC C22 H22 N2 O7 Cc1c2cccc(....
10 2FJ1 - CTC C22 H23 Cl N2 O8 C[C@]1(c2c....
11 5FKL - TDC C22 H22 N2 O7 Cc1c2cccc(....
12 2XB5 - I7T C21 H21 I N2 O7 CN(C)[C@H]....
13 2TRT - TAC C22 H24 N2 O8 C[C@]1(c2c....
14 4D7N Ka = 23000000 M^-1 TDC C22 H22 N2 O7 Cc1c2cccc(....
15 5FKM - TDC C22 H22 N2 O7 Cc1c2cccc(....
16 2VKE - TAC C22 H24 N2 O8 C[C@]1(c2c....
17 2O7O - DXT C22 H24 N2 O8 C[C@H]1c2c....
18 3FK7 Kd = 0.75 nM 4DM C20 H17 N O7 Cc1c2cccc(....
19 2X6O - 2TC C22 H21 Cl N2 O7 C[C@@]1(c2....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TDC; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 TDC 1 1
2 4DM 0.581395 0.762712
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2VPR; Ligand: TDC; Similar sites found: 261
This union binding pocket(no: 1) in the query (biounit: 2vpr.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2W3L DRO 0.006495 0.43643 None
2 1PR9 NAP 0.002491 0.42255 None
3 3D3W NAP 0.002241 0.4217 None
4 2QLX RM4 0.01187 0.42069 None
5 2ALG HP6 0.00173 0.41156 None
6 2ALG DAO 0.00173 0.41156 None
7 1POC GEL 0.001198 0.41108 None
8 4BI7 PGA 0.0005012 0.40057 None
9 2AQJ TRP 0.009026 0.42152 0.966184
10 1WGC SIA GAL BGC 0.01886 0.42081 1.16959
11 1ULE GLA GAL NAG 0.01986 0.40583 1.33333
12 1DSS NAD 0.002901 0.41027 1.44928
13 1U7Z PMT 0.006497 0.4066 1.44928
14 1XE7 GUN 0.007323 0.43385 1.47783
15 2YLD CMO 0.00291 0.43122 1.5748
16 3K3K A8S 0.0004755 0.42966 1.89573
17 1V6A TRE 0.005319 0.41389 1.93237
18 1EDO NAP 0.02117 0.41163 1.93237
19 1OTH PAO 0.006687 0.40493 1.93237
20 3F81 STT 0.03368 0.40089 2.18579
21 3OIG NAD 0.02242 0.40577 2.25564
22 1W3R PYR 0.02387 0.40202 2.31481
23 4CCO OGA 0.0005987 0.44719 2.41546
24 1A8R GTP 0.0006814 0.42408 2.41546
25 1WNG SAH 0.0006902 0.42388 2.41546
26 2YVF NAD 0.01739 0.41165 2.41546
27 2VBQ BSJ 0.004519 0.41384 2.42424
28 1QJC PNS 0.0238 0.401 2.53165
29 3JQM GTP 0.0005002 0.40224 2.54777
30 1N9L FMN 0.000393 0.4122 2.75229
31 1VDC FAD 0.001383 0.44755 2.89855
32 1SB8 NAD 0.004499 0.42693 2.89855
33 1SB8 UD2 0.009184 0.41759 2.89855
34 1F8F NAD 0.0121 0.41415 2.89855
35 3QV9 QV7 0.005343 0.41381 2.89855
36 1V35 NAI 0.00861 0.41028 2.89855
37 1R18 SAH 0.00214 0.41007 2.89855
38 1EYE PMM 0.002988 0.40361 2.89855
39 3TN7 NJP 0.006841 0.40331 2.89855
40 1I2B NAD 0.02303 0.40263 2.89855
41 1I2B UPG 0.02303 0.40263 2.89855
42 1I2B USQ 0.02303 0.40263 2.89855
43 3SIX GDP 0.003352 0.40175 2.89855
44 4L7I SAM 0.001294 0.40094 2.89855
45 3HF3 FMN 0.003995 0.40024 2.89855
46 1V7R CIT 0.01809 0.42175 3.22581
47 1I0Z OXM 0.001672 0.46555 3.38164
48 4OYA 1VE 0.00235 0.46521 3.38164
49 3MAG 3MA 0.00281 0.46364 3.38164
50 4QDC ASD 0.000291 0.44971 3.38164
51 2NX1 PEP 0.0003473 0.44768 3.38164
52 2NX1 RP5 0.0003776 0.44633 3.38164
53 1EB9 HBA 0.0003252 0.43927 3.38164
54 2AMV BIN 0.002481 0.43908 3.38164
55 4RJK PYR 0.006373 0.42931 3.38164
56 1UOU CMU 0.000261 0.42727 3.38164
57 1D6H COA 0.003988 0.42542 3.38164
58 2Z9V PXM 0.002946 0.41897 3.38164
59 1TDF FAD 0.008567 0.41482 3.38164
60 1TDF NAP 0.01977 0.41401 3.38164
61 4KQI RBZ 0.003594 0.41392 3.38164
62 4KQI NIO 0.003594 0.41392 3.38164
63 3LZW FAD 0.006269 0.41274 3.38164
64 2DTX BMA 0.006759 0.41248 3.38164
65 1E7S NAP 0.004583 0.41118 3.38164
66 1I7L ATP 0.002293 0.41074 3.38164
67 1GJW GLC 0.01382 0.40715 3.38164
68 3WE0 FAD 0.01214 0.40617 3.38164
69 3JQ3 ADP 0.003493 0.40573 3.38164
70 2WQP WQP 0.004435 0.40495 3.38164
71 3UER TUR 0.0008923 0.40332 3.38164
72 3UER BTU 0.0008923 0.40332 3.38164
73 2Q2V NAD 0.007964 0.40322 3.38164
74 2YN4 39J 0.01726 0.40284 3.38164
75 3C1O NAP 0.004923 0.40023 3.38164
76 1ECM TSA 0.0007169 0.43781 3.66972
77 1RZM PEP 0.00009347 0.48008 3.86473
78 2ZWS PLM 0.00416 0.46486 3.86473
79 1RZM E4P 0.00167 0.44897 3.86473
80 3P3N AKG 0.001511 0.44368 3.86473
81 3ZPG 5GP 0.006007 0.43811 3.86473
82 2PT9 2MH 0.001157 0.43658 3.86473
83 1XX4 BAM 0.009059 0.42928 3.86473
84 1P9P SAH 0.001202 0.41915 3.86473
85 1YBH FAD 0.00605 0.41437 3.86473
86 4KCT PYR 0.002855 0.41413 3.86473
87 1TUV VK3 0.01854 0.41384 3.86473
88 2NLI LAC 0.01104 0.4128 3.86473
89 2NLI FMN 0.01104 0.4128 3.86473
90 1H82 FAD 0.0156 0.41099 3.86473
91 1H82 GZZ 0.01741 0.41099 3.86473
92 2Q37 3AL 0.006848 0.40925 3.86473
93 2YC5 6BC 0.007461 0.40658 3.86473
94 3ZRR PXG 0.002439 0.40429 3.86473
95 2PT9 S4M 0.004975 0.40161 3.86473
96 3R35 4CO 0.0007485 0.43974 3.97351
97 1JUV NDP 0.005586 0.40123 4.14508
98 1Q0H FOM 0.002278 0.437 4.18719
99 1Q0H NDP 0.003639 0.43064 4.18719
100 1H8G CHT 0.02984 0.41819 4.21053
101 1MDZ DCS 0.001545 0.43048 4.34783
102 2Q8H TF4 0.01245 0.42243 4.34783
103 1ZK7 FAD 0.005969 0.42026 4.34783
104 1MDZ PLP 0.00358 0.41527 4.34783
105 1B8U OAA 0.005468 0.40826 4.34783
106 1TIW FAD 0.009166 0.40628 4.34783
107 1TIW TFB 0.009166 0.40628 4.34783
108 1IYE PGU 0.006635 0.40382 4.34783
109 1BTN I3P 0.00157 0.49468 4.71698
110 2C1Q BTN 0.01122 0.40382 4.7619
111 3UEC ALA ARG TPO LYS 0.008878 0.41594 4.79452
112 2F2U M77 0.000208 0.45253 4.83092
113 3BW2 FMN 0.002599 0.41791 4.83092
114 3B20 NAD 0.001917 0.41691 4.83092
115 1RYI GOA 0.008781 0.41178 4.83092
116 1RYI FAD 0.01333 0.40276 4.83092
117 4N02 FNR 0.02396 0.40053 4.83092
118 4NM5 ADP 0.004053 0.40001 4.83092
119 3NCQ ATP 0.001949 0.4097 5.04202
120 1ZZ7 S0H 0.001623 0.42953 5.05051
121 1C1L GAL BGC 0.0008672 0.46191 5.10949
122 1QY1 PRZ 0.0001666 0.44812 5.17241
123 1EP2 ORO 0.000702 0.4449 5.31401
124 1Y42 TYR 0.001063 0.43702 5.31401
125 2GSD NAD 0.001737 0.43103 5.31401
126 2XDQ MGX 0.009624 0.42798 5.31401
127 4GYW UDP 0.002089 0.42547 5.31401
128 1QF5 RPL 0.008081 0.41667 5.31401
129 1QF5 GDP 0.008081 0.41667 5.31401
130 4KCF AKM 0.001628 0.41616 5.31401
131 3I0O ADP 0.002008 0.41492 5.31401
132 2C7G ODP 0.01358 0.41209 5.31401
133 2C7G FAD 0.01413 0.41209 5.31401
134 1QPB TPP 0.003479 0.40887 5.31401
135 1LVL FAD 0.01242 0.40577 5.31401
136 3H22 B53 0.001193 0.40368 5.31401
137 4O1M NAD 0.006666 0.40246 5.31401
138 1EP2 FMN 0.005818 0.40199 5.31401
139 2C31 ADP 0.0414 0.40026 5.31401
140 2OYS FMN 0.002718 0.4045 5.78512
141 1RP0 AHZ 0.003455 0.44488 5.7971
142 2Y6P CTP 0.0009436 0.42745 5.7971
143 2XVE FAD 0.01177 0.41874 5.7971
144 1M5B BN1 0.01253 0.41494 5.7971
145 1TUF AZ1 0.002381 0.41181 5.7971
146 1SQ5 ADP 0.003242 0.40229 5.7971
147 2IXB A2G 0.01292 0.40044 5.7971
148 1SS4 GSH 0.004766 0.46659 5.88235
149 2O66 FLC 0.004914 0.41535 5.92593
150 3S9K CIT 0.00121 0.48246 5.9322
151 1Y75 NAG 0.005689 0.4023 5.9322
152 4C6F NCD 0.0002341 0.45057 6.28019
153 1G0N NDP 0.003223 0.42403 6.28019
154 1ML4 PAL 0.002217 0.41212 6.28019
155 1G0N PHH 0.009409 0.40875 6.28019
156 2HGS ADP 0.002365 0.4085 6.28019
157 1OLS TDP 0.01148 0.40801 6.28019
158 3LTW HLZ 0.0105 0.40676 6.28019
159 1JCM 137 0.005232 0.4051 6.28019
160 4R33 TRP 0.008243 0.40264 6.28019
161 4R33 SAH 0.008243 0.40264 6.28019
162 4AMV F6R 0.0018 0.40263 6.28019
163 2J07 HDF 0.02041 0.40116 6.28019
164 2J07 FAD 0.02041 0.40116 6.28019
165 4AF0 IMP 0.02062 0.40021 6.28019
166 3WO0 ADP 0.01173 0.40005 6.28019
167 3WO0 ALA 0.01173 0.40005 6.28019
168 4B9E FAH 0.001709 0.44851 6.31229
169 3BY8 MLT 0.001568 0.45022 6.33803
170 2GJ3 FAD 0.001788 0.41289 6.66667
171 2YPO PHE 0.0003822 0.44929 6.76329
172 2BLE 5GP 0.002627 0.44439 6.76329
173 4E28 9MZ 0.003686 0.42671 6.76329
174 2D0V PQQ 0.0006693 0.42435 6.76329
175 3GTD MLI 0.003609 0.42102 6.76329
176 4E28 0MZ 0.00499 0.41507 6.76329
177 3P7I P7I 0.004699 0.41068 6.76329
178 1R6D NAD 0.01915 0.40524 6.76329
179 4PO2 ASN ARG LEU LEU LEU THR GLY 0.003251 0.40349 6.76329
180 2YBQ SAH 0.002616 0.4032 6.76329
181 2YBQ UP2 0.01066 0.40165 6.76329
182 2PWY SAH 0.004259 0.40092 6.76329
183 1O9U ADZ 0.004251 0.44553 7.24638
184 2EB5 OXL 0.004165 0.42439 7.24638
185 3K37 BCZ 0.0164 0.41963 7.24638
186 3DGB MUC 0.001463 0.41509 7.24638
187 4LSJ LSJ 0.001866 0.41038 7.24638
188 3D2Y AH0 ALA FGA LYS 0.0004736 0.40898 7.24638
189 1R37 NAD 0.00696 0.40662 7.24638
190 1I36 NAP 0.003062 0.40615 7.24638
191 2NCD ADP 0.009977 0.40232 7.24638
192 1E5F PLP 0.00194 0.40149 7.24638
193 2ZB3 NDP 0.006584 0.40135 7.24638
194 3H86 AP5 0.001277 0.44753 7.29167
195 1F5F DHT 0.0006774 0.41979 7.31707
196 2Q09 DI6 0.0005189 0.44334 7.72947
197 2V7T SAH 0.01386 0.42776 7.72947
198 4M51 BEZ 0.007099 0.42709 7.72947
199 3FXU TSU 0.002526 0.41087 7.72947
200 2HGZ PBF 0.004074 0.40325 7.72947
201 1MQ0 BRD 0.0009925 0.4027 7.85714
202 2PTZ PAH 0.0001096 0.44501 8.21256
203 2QCX PF1 0.001213 0.44102 8.21256
204 1KBJ FMN 0.0006611 0.43397 8.21256
205 2Q1A 2KT 0.003495 0.42773 8.21256
206 3Q9T FAY 0.007 0.41087 8.21256
207 1ECC PCP 0.003526 0.40391 8.21256
208 1KDK DHT 0.000714 0.42734 8.47458
209 3RF4 FUN 0.001734 0.42836 8.62069
210 3FC4 EDO 0.0008317 0.46093 8.69565
211 2B7N NTM 0.0004478 0.45929 8.69565
212 1Z44 NPO 0.01793 0.43032 8.69565
213 1RYD NDP 0.006969 0.4099 8.69565
214 3BRE C2E 0.009195 0.4093 8.69565
215 1Z45 NAD 0.005402 0.40591 8.69565
216 1H6C NDP 0.00891 0.40574 8.69565
217 2R40 20E 0.003598 0.40523 8.69565
218 2Y7P SAL 0.001281 0.43372 8.7156
219 1ME8 RVP 0.005494 0.44105 9.17874
220 3I51 45C 0.001118 0.41942 9.17874
221 3TFC PEP 0.0000388 0.49564 9.66184
222 2TPL HPP 0.0005665 0.43644 9.66184
223 2XK9 XK9 0.001531 0.43191 9.66184
224 3W54 RNB 0.0006316 0.41287 9.66184
225 2JFV FLC 0.009662 0.40835 9.96564
226 3GE7 AFQ 0.004499 0.41272 10.1449
227 1FIQ FAD 0.001529 0.43192 10.628
228 3KJI ADP 0.001041 0.41092 10.628
229 4G1V FAD 0.004301 0.40689 10.628
230 4JWX 1N4 0.007258 0.40296 10.628
231 1JIL 485 0.002741 0.40248 10.628
232 4M5P MLA 0.003852 0.45656 11.1111
233 4M5P 23W 0.005846 0.43109 11.1111
234 4LTN FMN 0.01686 0.40046 11.1675
235 1OFH ADP 0.01643 0.41074 11.4943
236 3OND NAD 0.003028 0.43385 11.5942
237 3OND ADN 0.003028 0.43385 11.5942
238 2IMP NAI 0.04049 0.4037 11.5942
239 3KO0 TFP 0.01956 0.4075 11.8812
240 3I28 34N 0.006187 0.4205 12.0773
241 1Q3Q ANP 0.01151 0.41646 12.0773
242 3DG6 MUC 0.001006 0.41615 12.0773
243 3MPI GRA 0.01904 0.40534 12.0773
244 1M7Y PPG 0.006489 0.4029 12.0773
245 1O7N IND 0.00387 0.40074 12.0773
246 2GDZ NAD 0.006079 0.40398 12.5604
247 3CF6 SP1 0.000304 0.42956 12.5749
248 1OAA OAA 0.008161 0.41305 13.5266
249 4N7C AEF 0.002364 0.4421 13.6364
250 1DR1 NAP 0.001444 0.4365 13.7566
251 1DR1 HBI 0.001444 0.4365 13.7566
252 1Q11 TYE 0.002467 0.42211 14.0097
253 1GU3 BGC BGC BGC BGC BGC 0.002543 0.42157 14.094
254 3TKA CTN 0.007879 0.44604 14.9758
255 3MTW M3R 0.001263 0.40799 16.9082
256 2EWM NAD 0.00187 0.42468 17.8744
257 3QDY CBS 0.00541 0.42574 18.1818
258 2FOI JPA 0.001353 0.42147 18.3333
259 4EPM AMP 0.004462 0.40018 18.8406
260 1T0S BML 0.001305 0.46192 22.093
261 2J5S KTA 0.001355 0.41135 23.6715
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